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Fetit R, Barbato MI, Theil T, Pratt T, Price DJ. 16p11.2 deletion accelerates subpallial maturation and increases variability in human iPSC-derived ventral telencephalic organoids. Development 2023; 150:dev201227. [PMID: 36826401 PMCID: PMC10110424 DOI: 10.1242/dev.201227] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023]
Abstract
Inhibitory interneurons regulate cortical circuit activity, and their dysfunction has been implicated in autism spectrum disorder (ASD). 16p11.2 microdeletions are genetically linked to 1% of ASD cases. However, few studies investigate the effects of this microdeletion on interneuron development. Using ventral telencephalic organoids derived from human induced pluripotent stem cells, we have investigated the effect of this microdeletion on organoid size, progenitor proliferation and organisation into neural rosettes, ganglionic eminence marker expression at early developmental timepoints, and expression of the neuronal marker NEUN at later stages. At early stages, deletion organoids exhibited greater variations in size with concomitant increases in relative neural rosette area and the expression of the ventral telencephalic marker COUPTFII, with increased variability in these properties. Cell cycle analysis revealed an increase in total cell cycle length caused primarily by an elongated G1 phase, the duration of which also varied more than normal. At later stages, deletion organoids increased their NEUN expression. We propose that 16p11.2 microdeletions increase developmental variability and may contribute to ASD aetiology by lengthening the cell cycle of ventral progenitors, promoting premature differentiation into interneurons.
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Affiliation(s)
- Rana Fetit
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Michela Ilaria Barbato
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Thomas Theil
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Thomas Pratt
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - David J. Price
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
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Szelest M, Stefaniak M, Ręka G, Jaszczuk I, Lejman M. Three case reports of patients indicating the diversity of molecular and clinical features of 16p11.2 microdeletion anomaly. BMC Med Genomics 2021; 14:76. [PMID: 33691695 PMCID: PMC7945342 DOI: 10.1186/s12920-021-00929-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 16p11.2 microdeletion is a known chromosomal anomaly associated mainly with neurocognitive developmental delay, predisposition to obesity, and variable dysmorphism. Although this deletion is relatively rare among the general population, it is one of the serious known genetic aetiologies of obesity and autism spectrum disorder. CASE PRESENTATION This study presents three cases of deletions within the 16p11.2 region. Every child had mild variable craniofacial abnormalities, hand or foot anomalies and developmental and language delays. The first proband had obesity, epilepsy, moderate intellectual disability, aphasia, motor delay, hyperinsulinism, and café au lait spots. The second proband suffered from cardiac, pulmonary, and haematological problems. The third proband had motor and language delays, bronchial asthma, and umbilical hernia. Although each patient presented some features of the syndrome, the children differed in terms of their clinical pictures. Genetic diagnosis of 16p11.2 microdeletion syndrome was made in children at different ages based on multiplex ligation probe-dependent amplification analysis and/or microarray methods. CONCLUSIONS Our reports allow us to analyse and better understand the biology of 16p11.2 microdeletion throughout development. However, the variability of presented cases supports the alternate conclusion to this presented in available literature regarding 16p11.2 deletion, as we observed no direct cause-and-effect genotype/phenotype relationships. The reported cases indicate the key role of the interdisciplinary approach in 16p11.2 deletion diagnostics. The care of patients with this anomaly is based on regular health assessment and adjustment of nervous system development therapy.
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Affiliation(s)
- Monika Szelest
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, Gębali 6, 20-093, Lublin, Poland
| | - Martyna Stefaniak
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, Gębali 6, 20-093, Lublin, Poland
| | - Gabriela Ręka
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, Gębali 6, 20-093, Lublin, Poland
| | - Ilona Jaszczuk
- Department of Cancer Genetics With Cytogenetics Laboratory, Medical University of Lublin, Radziwiłłowska 11, 20-080, Lublin, Poland
| | - Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, A. Gębali 6, 20-093, Lublin, Poland.
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Linhares ND, Freire MCM, Cardenas RGCDCL, Pena HB, Lachlan K, Dallapiccola B, Bacino C, Delobel B, James P, Thuresson AC, Annerén G, Pena SDJ. 1p13.2 deletion displays clinical features overlapping Noonan syndrome, likely related to NRAS gene haploinsufficiency. Genet Mol Biol 2016; 39:349-57. [PMID: 27561113 PMCID: PMC5004838 DOI: 10.1590/1678-4685-gmb-2016-0049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/09/2016] [Indexed: 11/22/2022] Open
Abstract
Deletion-induced hemizygosity may unmask deleterious autosomal recessive variants and be a cause of the phenotypic variability observed in microdeletion syndromes. We performed complete exome sequencing (WES) analysis to examine this possibility in a patient with 1p13.2 microdeletion. Since the patient displayed clinical features suggestive of Noonan Syndrome (NS), we also used WES to rule out the presence of pathogenic variants in any of the genes associated with the different types of NS. We concluded that the clinical findings could be attributed solely to the 1p13.2 haploinsufficiency. Retrospective analysis of other nine reported patients with 1p13.2 microdeletions showed that six of them also presented some characteristics of NS. In all these cases, the deleted segment included the NRAS gene. Gain-of-function mutations of NRAS gene are causally related to NS type 6. Thus, it is conceivable that NRAS haploinsufficiency and gain-of-function mutations may have similar clinical consequences. The same phenomenon has been described for two other genes belonging to the Ras/MAPK pathway: MAP2K2 and SHOC2. In conclusion, we here report genotype-phenotype correlations in patients with chromosome 1p13.2 microdeletions and we propose that NRAS may be a critical gene for the NS characteristics in the patients.
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Affiliation(s)
- Natália Duarte Linhares
- Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Maíra Cristina Menezes Freire
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | | | | | - Katherine Lachlan
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
| | | | - Carlos Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Bruno Delobel
- Centre de Génétique Chromosomique, GH de l'Institut Catholique de Lille - Hopital Saint Vincent de Paul, Lille, France
| | - Paul James
- Victorian Clinical Genetics Service, Melbourne, Victoria, Australia
| | - Ann-Charlotte Thuresson
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Sérgio D J Pena
- Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.,Laboratório Gene - Núcleo de Genética Médica, Belo Horizonte, MG, Brazil
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Unmasking a novel disease gene NEO1 associated with autism spectrum disorders by a hemizygous deletion on chromosome 15 and a functional polymorphism. Behav Brain Res 2016; 300:135-42. [DOI: 10.1016/j.bbr.2015.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 10/14/2015] [Accepted: 10/21/2015] [Indexed: 11/20/2022]
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Barea JJ, van Meel E, Kornfeld S, Bird LM. Tuberous sclerosis, polycystic kidney disease and mucolipidosis III gamma caused by a microdeletion unmasking a recessive mutation. Am J Med Genet A 2015; 167A:2844-6. [PMID: 26108976 PMCID: PMC4708255 DOI: 10.1002/ajmg.a.37213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/04/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Jaime J. Barea
- Department of Pediatrics, University of California, San Diego, California
- Division of Dysmorphology/Genetics, Rady Children’s Specialists of San Diego, San Diego, California
| | - Eline van Meel
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Stuart Kornfeld
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Lynne M. Bird
- Department of Pediatrics, University of California, San Diego, California
- Division of Dysmorphology/Genetics, Rady Children’s Specialists of San Diego, San Diego, California
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Linhares ND, Svartman M, Rodrigues TC, Rosenberg C, Valadares ER. Subtelomeric 6p25 deletion/duplication: Report of a patient with new clinical findings and genotype–phenotype correlations. Eur J Med Genet 2015; 58:310-8. [DOI: 10.1016/j.ejmg.2015.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 02/28/2015] [Indexed: 01/02/2023]
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Czeschik JC, Hehr U, Hartmann B, Lüdecke HJ, Rosenbaum T, Schweiger B, Wieczorek D. 160 kb deletion in ISPD unmasking a recessive mutation in a patient with Walker–Warburg syndrome. Eur J Med Genet 2013; 56:689-94. [DOI: 10.1016/j.ejmg.2013.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/30/2013] [Indexed: 01/03/2023]
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An unusual clinical severity of 16p11.2 deletion syndrome caused by unmasked recessive mutation of CLN3. Eur J Hum Genet 2013; 22:369-73. [PMID: 23860047 DOI: 10.1038/ejhg.2013.141] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 05/29/2013] [Accepted: 06/03/2013] [Indexed: 01/09/2023] Open
Abstract
With the introduction of array comparative genomic hybridization (aCGH) techniques in the diagnostic setting of patients with developmental delay and congenital malformations, many new microdeletion syndromes have been recognized. One of these recently recognized microdeletion syndromes is the 16p11.2 deletion syndrome, associated with variable clinical outcomes including developmental delay, autism spectrum disorder, epilepsy, and obesity, but also apparently normal phenotype. We report on a 16-year-old patient with developmental delay, exhibiting retinis pigmentosa with progressive visual failure from the age of 9 years, ataxia, and peripheral neuropathy. Chromosomal microarray analysis identified a 1.7-Mb 16p11.2 deletion encompassing the 593-kb common deletion (∼29.5 to ∼30.1 Mb; Hg18) and the 220-kb distal deletion (∼28.74 to ∼28.95 Mb; Hg18) that partially included the CLN3 gene. As the patient's clinical findings were different from usual 16p11.2 microdeletion phenotypes and showed some features reminiscent of juvenile neuronal ceroid-lipofuscinosis (JNCL, Batten disease, OMIM 204200), we suspected and confirmed a mutation of the remaining CLN3 allele. This case further illustrates that unmasking of hemizygous recessive mutations by chromosomal deletion represents one explanation for the phenotypic variability observed in chromosomal deletion disorders.
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Shaffer LG, Dabell MP, Fisher AJ, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Rosenfeld JA. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn 2012; 32:976-85. [PMID: 22865506 PMCID: PMC3491694 DOI: 10.1002/pd.3945] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/11/2012] [Accepted: 07/01/2012] [Indexed: 01/12/2023]
Abstract
Objective To demonstrate the usefulness of microarray testing in prenatal diagnosis based on our laboratory experience. Methods Prenatal samples received from 2004 to 2011 for a variety of indications (n = 5003) were tested using comparative genomic hybridization-based microarrays targeted to known chromosomal syndromes with later versions of the microarrays providing backbone coverage of the entire genome. Results The overall detection rate of clinically significant copy number alterations (CNAs) among unbiased, nondemise cases was 5.3%. Detection rates were 6.5% and 8.2% for cases referred with abnormal ultrasounds and fetal demise, respectively. The overall rate of findings with unclear clinical significance was 4.2% but would reduce to 0.39% if only de novo CNAs were considered. In cases with known chromosomal rearrangements in the fetus or parent, 41.1% showed CNAs related to the rearrangements, whereas 1.3% showed clinically significant CNAs unrelated to the karyotype. Finally, 71% of the clinically significant CNAs found by microarray were below the resolution of conventional karyotyping of fetal chromosomes. Conclusions Microarray analysis has advantages over conventional cytogenetics, including the ability to more precisely characterize CNAs associated with abnormal karyotypes. Moreover, a significant proportion of cases studied by array will show a clinically significant CNA even with apparently normal karyotypes. © 2012 John Wiley & Sons, Ltd.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA.
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Poot M. Beware of Hemizygous Deletions That May Unmask Deleterious Variants. Mol Syndromol 2012; 3:45-46. [PMID: 23112749 DOI: 10.1159/000339564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Abstract
Zusammenfassung
Die Ursache neurokognitiver Entwicklungsstörungen mit Intelligenzminderung stellt eine der häufigsten Fragestellungen in der genetischen Sprechstunde dar. Obwohl mehr als 400 krankheitsverursachende Einzelgendefekte bekannt sind, machen Chromosomenaberrationen derzeit den größten Anteil der bekannten Ursachen aus. Mittels hochauflösender Array-Techniken lassen sich nach Ausschluss des Down-Syndroms bei unselektionierten Patienten in 18% der Fälle relevante chromosomale Imbalancen nachweisen, wobei die Aberrationen nur in 4% der Fälle auch primär mikroskopisch sichtbar wären. Mit zunehmender Auflösung steigt jedoch auch die Rate an detektierten Kopienzahl-Normvarianten, welche die Beurteilung der Befunde erschweren können. Indikatoren für krankheitsrelevante Aberrationen sind Aberrationsgröße, Gengehalt und Segregation innerhalb der Familie. Eine Kausalität kann letztlich aber nur dann belegt werden, wenn Vergleichsfälle mit ähnlichem Genotyp und Phänotyp vorliegen.
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Shimada S, Miya K, Oda N, Watanabe Y, Kumada T, Sugawara M, Shimojima K, Yamamoto T. An unmasked mutation of EIF2B2 due to submicroscopic deletion of 14q24.3 in a patient with vanishing white matter disease. Am J Med Genet A 2012; 158A:1771-7. [PMID: 22678813 DOI: 10.1002/ajmg.a.35431] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/29/2012] [Indexed: 12/21/2022]
Abstract
Leukodystrophy with vanishing white matter (VWM) is a neurodegenerative disorder with autosomal recessive traits that is caused by alteration of the eukaryotic translation initiation factor-2B (EIF2B). An 11-month-old patient with distinctive features began to exhibit progressive developmental deterioration associated with intractable epilepsy, which was triggered by recurrent acute infectious diseases. Brain magnetic resonance imaging (MRI) revealed abnormal white matter intensity. Chromosomal microarray testing identified a submicroscopic deletion at 14q24.3 that included EIF2B2, the gene encoding one of the subunits of EIF2B. Because the patient's clinical findings were distinctive for VWM, compound heterozygous mutations of EIF2B2 were suspected, and subsequent sequencing analysis of the remaining allele unmasked the existence of a novel missense mutation of EIF2B2 (V85W). Some distinctive features including small palpebral fissures, bushy eyebrows, ear abnormalities, small upturned nose, downturned corners of the mouth, and micrognathia may be the common features of the patients with 14q24.3 deletions.
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Affiliation(s)
- Shino Shimada
- Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan
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Abstract
Array-based genome-wide segmental aneuploidy screening detects both de novo and inherited copy number variations (CNVs). In sporadic patients de novo CNVs are interpreted as potentially pathogenic. However, a deletion, transmitted from a healthy parent, may be pathogenic if it overlaps with a mutated second allele inherited from the other healthy parent. To detect such events, we performed multiplex enrichment and next-generation sequencing of the entire coding sequence of all genes within unique hemizygous deletion regions in 20 patients (1.53 Mb capture footprint). Out of the detected 703 non-synonymous single-nucleotide variants (SNVs), 8 represented variants being unmasked by a hemizygous deletion. Although evaluation of inheritance patterns, Grantham matrix scores, evolutionary conservation and bioinformatic predictions did not consistently indicate pathogenicity of these variants, no definitive conclusions can be drawn without functional validation. However, in one patient with severe mental retardation, lack of speech, microcephaly, cheilognathopalatoschisis and bilateral hearing loss, we discovered a second smaller deletion, inherited from the other healthy parent, resulting in loss of both alleles of the highly conserved heat shock factor binding protein 1 (HSBP1) gene. Conceivably, inherited deletions may unmask rare pathogenic variants that may exert a phenotypic impact through a recessive mode of gene action.
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News Briefs. Genet Med 2012. [DOI: 10.1038/gim.2011.74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Gijsbers ACJ, Schoumans J, Ruivenkamp CAL. Interpretation of array comparative genome hybridization data: a major challenge. Cytogenet Genome Res 2011; 135:222-7. [PMID: 22086107 DOI: 10.1159/000334066] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The advent and application of high-resolution array-based comparative genome hybridization (array CGH) has led to the detection of large numbers of copy number variants (CNVs) in patients with developmental delay and/or multiple congenital anomalies as well as in healthy individuals. The notion that CNVs are also abundantly present in the normal population challenges the interpretation of the clinical significance of detected CNVs in patients. In this review we will illustrate a general clinical workflow based on our own experience that can be used in routine diagnostics for the interpretation of CNVs.
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Affiliation(s)
- A C J Gijsbers
- Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Array comparative genomic hybridization analysis in patients with anophthalmia, microphthalmia, and coloboma. Genet Med 2011; 13:437-42. [PMID: 21285886 DOI: 10.1097/gim.0b013e318204cfd2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE The goal of our study was to determine whether genomic copy number abnormalities (deletions and duplications) affecting genes involved in eye development contributed to the etiology of anophthalmia, microphthalmia, and coloboma. METHODS The affected individuals were evaluated for the presence of deletions and duplications in genomic DNA by a very high-resolution array comparative genomic hybridization. RESULTS Array analysis of 32 patients detected one case with a deletion encompassing the renal-coloboma syndrome associated gene PAX2. Nonpolymorphic copy number changes were also observed at several candidate chromosomal regions, including 6p12.3, 8q23.1q23.2, 13q31.3, 15q11.2q13.1, 16p13.13, and 20q13.13. CONCLUSIONS This study identified the first patient with the typical phenotype of the renal-coloboma syndrome caused by a submicroscopic deletion of the coding region of the PAX2 gene. The finding suggests that PAX2 deletion testing should be performed in addition to gene sequencing as a part of molecular evaluation for the renal-coloboma syndrome. Array comparative genomic hybridization testing of 32 affected individuals showed that genomic deletions and duplications are not a common cause of nonsyndromic anophthalmia, microphthalmia, or coloboma but undoubtedly contribute to the etiology of these eye anomalies. Therefore, array comparative genomic hybridization testing represents an important and valuable addition to candidate gene sequencing in research and diagnostics of ocular birth defects.
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Colnaghi R, Carpenter G, Volker M, O'Driscoll M. The consequences of structural genomic alterations in humans: genomic disorders, genomic instability and cancer. Semin Cell Dev Biol 2011; 22:875-85. [PMID: 21802523 DOI: 10.1016/j.semcdb.2011.07.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 07/11/2011] [Accepted: 07/14/2011] [Indexed: 12/20/2022]
Abstract
Over the last decade or so, sophisticated technological advances in array-based genomics have firmly established the contribution of structural alterations in the human genome to a variety of complex developmental disorders, and also to diseases such as cancer. In fact, multiple 'novel' disorders have been identified as a direct consequence of these advances. Our understanding of the molecular events leading to the generation of these structural alterations is also expanding. Many of the models proposed to explain these complex rearrangements involve DNA breakage and the coordinated action of DNA replication, repair and recombination machinery. Here, and within the context of Genomic Disorders, we will briefly overview the principal models currently invoked to explain these chromosomal rearrangements, including Non-Allelic Homologous Recombination (NAHR), Fork Stalling Template Switching (FoSTeS), Microhomology Mediated Break-Induced Repair (MMBIR) and Breakage-fusion-bridge cycle (BFB). We will also discuss an unanticipated consequence of certain copy number variations (CNVs) whereby the CNVs potentially compromise fundamental processes controlling genomic stability including DNA replication and the DNA damage response. We will illustrate these using specific examples including Genomic Disorders (DiGeorge/Veleocardiofacial syndrome, HSA21 segmental aneuploidy and rec (3) syndrome) and cell-based model systems. Finally, we will review some of the recent exciting developments surrounding specific CNVs and their contribution to cancer development as well as the latest model for cancer genome rearrangement; 'chromothripsis'.
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Affiliation(s)
- Rita Colnaghi
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
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A three-step workflow procedure for the interpretation of array-based comparative genome hybridization results in patients with idiopathic mental retardation and congenital anomalies. Genet Med 2010; 12:478-85. [PMID: 20734469 DOI: 10.1097/gim.0b013e3181e3914a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
One of the aims of clinical genetics is to identify gene mutations or genomic rearrangements that may underlie complex presentations of phenotypic features, such as multiple congenital malformations and mental retardation. During the decade after publication of the first article on array-based comparative genome hybridization, this technique has supplemented karyotyping as the prime genome-wide screening method in patients with idiopathic multiple congenital malformations and mental retardation. The use of this novel, discovery-based, approach has dramatically increased the detection rate of genomic imbalances. Array-based comparative genome hybridization detects copy number changes in the genome of patients and healthy subjects, some of which may represent phenotypically neutral copy number variations. This prompts the need for properly distinguishing between those copy number changes that may contribute to the clinical phenotype amid a pool of neutral copy number variations. We briefly review the characteristics of copy number changes in relation to their clinical relevance. Second, we discuss several published workflow schemes to identify copy number changes putatively contributing to the phenotype, and third, we propose a three-step procedure aiming to rapidly evaluate copy number changes on a case-by-case basis as to their potential contribution to the phenotype of patients with idiopathic multiple congenital malformations and mental retardation. This workflow is gene-centered and should aid in identification of disease-related candidate genes and in estimating the recurrence risk for the disorder in the family.
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Buysse K, Vergult S, Mussche S, Groote CCD, Speleman F, Menten B, Lissens W, Van Coster R. Giant axonal neuropathy caused by compound heterozygosity for a maternally inherited microdeletion and a paternal mutation within the GAN gene. Am J Med Genet A 2010; 152A:2802-4. [DOI: 10.1002/ajmg.a.33508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Edelmann L, Hirschhorn K. Clinical Utility of Array CGH for the Detection of Chromosomal Imbalances Associated with Mental Retardation and Multiple Congenital Anomalies. Ann N Y Acad Sci 2008; 1151:157-66. [DOI: 10.1111/j.1749-6632.2008.03610.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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A novel genomic disorder: a deletion of the SACS gene leading to Spastic Ataxia of Charlevoix–Saguenay. Eur J Hum Genet 2008; 16:1050-4. [DOI: 10.1038/ejhg.2008.58] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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