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Riviello FN, Daponte A, Ponzi E, Ficarella R, Orsini P, Bucci R, Ventura M, Antonacci F, Catacchio CR, Gentile M. A Rare Case of Concurrent 2q34q36 Duplication and 2q37 Deletion in a Neonate with Syndromic Features. Genes (Basel) 2023; 14:2194. [PMID: 38137016 PMCID: PMC10742419 DOI: 10.3390/genes14122194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Large-scale genomic structural variations can have significant clinical implications, depending on the specific altered genomic region. Briefly, 2q37 microdeletion syndrome is a prevalent subtelomeric deletion disorder characterized by variable-sized deletions. Affected patients exhibit a wide range of clinical manifestations, including short stature, facial dysmorphism, and features of autism spectrum disorder, among others. Conversely, isolated duplications of proximal chromosome 2q are rare and lack a distinct phenotype. In this report, we provide an extensive molecular analysis of a 15-day-old newborn referred for syndromic features. Our analysis reveals an 8.5 Mb microdeletion at 2q37.1, which extends to the telomere, in conjunction with an 8.6 Mb interstitial microduplication at 2q34q36.1. Our findings underscore the prominence of 2q37 terminal deletions as commonly reported genomic anomalies. We compare our patient's phenotype with previously reported cases in the literature to contribute to a more refined classification of 2q37 microdeletion syndrome and assess the potential impact of 2q34q36.1 microduplication. We also investigate multiple hypotheses to clarify the genetic mechanisms responsible for the observed genomic rearrangement.
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Affiliation(s)
- Francesco Nicola Riviello
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Alessia Daponte
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Emanuela Ponzi
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Romina Ficarella
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Paola Orsini
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Roberta Bucci
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Mario Ventura
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Francesca Antonacci
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Claudia Rita Catacchio
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Mattia Gentile
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
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Ismail A, Ahid F, Thong MK, Zakaria Z. Terminal microdeletion of chromosome 18 in a Malaysian boy characterized with few features of typical 18q- deletion syndrome: a case report. J Med Case Rep 2023; 17:250. [PMID: 37296475 DOI: 10.1186/s13256-023-03984-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 05/13/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND The 18q- deletion syndrome is a rare congenital chromosomal disorder caused by a partial deletion of the long arm of chromosome 18. The diagnosis of a patient with this syndrome relies on the family medical history, physical examination, developmental assessment, and cytogenetic findings. However, the phenotype of patients with 18q- deletion syndrome can be highly variable, ranging from almost normal to severe malformations and intellectual disability, and normal cytogenetic findings are common, thus complicating the diagnosis. Interestingly, only few characteristic features of typical 18q- deletion syndrome were found in the patient, despite sharing the same critical region. To our knowledge, this is the first report of a Malaysian individual with 18q- terminal microdeletion diagnosed with microarray-based technology. CASE PRESENTATION Here we report a 16-year-old Malaysian Chinese boy, a product of a non-consanguineous marriage, who presented with intellectual disability, facial dysmorphism, high arched palate, congenital talipes equinovarus (clubfoot), congenital scoliosis, congenital heart defect, and behavioral problems. A routine chromosome analysis on 20 metaphase cells showed a normal 46, XY G-banded karyotype. Array-based comparative genomic hybridization was performed using a commercially available 244 K 60-mer oligonucleotide microarray slide according to the manufacturer's protocol. This platform allows genome-wide survey and molecular profiling of genomic aberrations with an average resolution of about 10 kB. In addition, multiplex ligation-dependent probe amplification analysis was carried out using SALSA MLPA kit P320 Telomere-13 to confirm the array-based comparative genomic hybridization finding. Array-based comparative genomic hybridization analysis revealed a 7.3 MB terminal deletion involving chromosome band 18q22.3-qter. This finding was confirmed by multiplex ligation-dependent probe amplification, where a deletion of ten probes mapping to the 18q22.3-q23 region was detected, and further multiplex ligation-dependent probe amplification analysis on his parents showed the deletion to be de novo. CONCLUSION The findings from this study expand the phenotypic spectrum of the 18q- deletion syndrome by presenting a variation of typical 18q- deletion syndrome features to the literature. In addition, this case report demonstrated the ability of the molecular karyotyping method, such as array-based comparative genomic hybridization, to assist in the diagnosis of cases with a highly variable phenotype and variable aberrations, such as 18q- deletion syndrome.
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Affiliation(s)
- Azli Ismail
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170, Shah Alam, Selangor, Malaysia
| | - Fadly Ahid
- Centre for Medical Laboratory Technology Studies, Faculty of Health Sciences, Universiti Teknologi MARA, 42300, Puncak Alam, Selangor, Malaysia.
- Stem Cell and Regenerative Medicine Research Initiative Group, Universiti Teknologi MARA, 40450, Shah Alam, Selangor, Malaysia.
| | - Meow-Keong Thong
- Department of Pediatrics, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Zubaidah Zakaria
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170, Shah Alam, Selangor, Malaysia
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Increased Diagnostic Yield of Array Comparative Genomic Hybridization for Autism Spectrum Disorder in One Institution in Taiwan. Medicina (B Aires) 2021; 58:medicina58010015. [PMID: 35056323 PMCID: PMC8779646 DOI: 10.3390/medicina58010015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Background and Objectives: Chromosomal microarray offers superior sensitivity for identification of submicroscopic copy number variants (CNVs) and is recommended for the initial genetic testing of patients with autism spectrum disorder (ASD). This study aims to determine the diagnostic yield of array comparative genomic hybridization (array-CGH) in ASD patients from a cohort of Chinese patients in Taiwan. Materials and Methods: Enrolled in this study were 80 ASD children (49 males and 31 females; 2–16 years old) followed up at Taipei MacKay Memorial Hospital between January 2010 and December 2020. The genomic DNA extracted from blood samples was analyzed by array-CGH via the Affymetrix GeneChip Genome-Wide Human single nucleotide polymorphism (SNP) and NimbleGen International Standards for Cytogenomic Arrays (ISCA) Plus Cytogenetic Arrays. The CNVs were classified into five groups: pathogenic (pathologic variant), likely pathogenic (potential pathologic variant), likely benign (potential normal genomic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance), according to the American College of Medical Genetics (ACMG) guidelines. Results: We identified 47 CNVs, 31 of which in 27 patients were clinically significant. The overall diagnostic yield was 33.8%. The most frequently clinically significant CNV was 15q11.2 deletion, which was present in 4 (5.0%) patients. Conclusions: In this study, a satisfactory diagnostic yield of array-CGH was demonstrated in a Taiwanese ASD patient cohort, supporting the clinical usefulness of array-CGH as the first-line testing of ASD in Taiwan.
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Clinical and molecular cytogenetic description of a female patient with de novo 18q inversion duplication/deletion. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Hogendorf A, Zieliński M, Constantinou M, Śmigiel R, Wierzba J, Wyka K, Wędrychowicz A, Jakubiuk-Tomaszuk A, Budzynska E, Piotrowicz M, Lipska-Ziętkiewicz BS, Kaczorowska E, Cieślikowska A, Kutkowska-Kaźmierczak A, Fijak-Moskal J, Kugaudo M, Kosińska-Urbańska M, Szadkowska A, Borowiec M, Niedźwiecki M, Trzonkowski P, Młynarski W. Immune Dysregulation in Patients With Chromosome 18q Deletions-Searching for Putative Loci for Autoimmunity and Immunodeficiency. Front Immunol 2021; 12:742834. [PMID: 34867966 PMCID: PMC8637865 DOI: 10.3389/fimmu.2021.742834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction Autoimmune disorders, IgA deficiency, and allergies seem to be common among individuals with 18q deletion syndrome [OMIM 601808]. We aimed to determine the prevalence, mechanism, and genetic background of autoimmunity, immune deficiency, and allergy in a cohort of patients with 18q deletions. Material and Methods Medical registries and social media were used to recruit the patients. Microarray oligonucleotide comparative genomic hybridization (aCGH) (Agilent, Santa Clara, CA, USA) was performed in all patients to identify size and location of chromosome 18 deletion. Clinical evaluation and medical record collection were performed in each of the study participants. The history of autoimmune disorders, severe and/or recurrent infections, and symptoms of allergy were noted. Total immunoglobulin IgG, IgA, IgM, IgE, and IgG1-4 serum levels were measured using nephelometry and ELISA methods. Lymphocyte T subset phenotyping was performed in 24 subjects from 18q del cohort. To predict the most promising candidate genes, we used the ENDEAVOUR-a free web resource for gene prioritization. Results 18q deletion was confirmed by means of array CGH analysis in 27 individuals, 15 (55.6%) females and 12 males, referred to the project by specialists in medical genetics, diabetology, or pediatric endocrinology between May 2015 and December 2019. The mean age at examination was 11.8 years (min-max: 4.0-33.5). Autoimmune disorders were present in 14/27 (51.8%) of the cohort. In eight of patients, symptoms of immune deficiency coexisted with autoimmunity. Allergy was reported in nine of 27 (33.4%) patients. Over 89% of patients presented with at list one type of immunoglobulin (IgA, IgM, IgG, IgE, and IgG1-4) deficiency and eight of 25 (32%) had abnormalities in at least two major immunoglobulin (IgG, IgA, IgM) measurements (CVID-like phenotype). Patients with 18q del exhibited a significantly decreased CD4, Treg FOXP3+, TregFOXP3+Helios+, and TemCD4 cell numbers in comparison with the control groups of 24 T1DM patients and 28 healthy controls. Conclusions Patients with 18q deletions frequently suffer from autoimmune disorders, recurrent infections, and allergy due to immune dysregulation presenting with variable antibody deficiencies and T-regulatory cell deficiency (CD4+CD25+CD127lowFOXP3+). The spectrum of speculations regarding which gene might be responsible for such phenotype ranges from single gene haploinsufficiency to deletion of a cluster of immunogenes located distally to 18q21.
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Affiliation(s)
- Anna Hogendorf
- Department of Pediatrics, Diabetology, Endocrinology and Nephrology, Medical University of Lodz, Lodz, Poland
| | - Maciej Zieliński
- Department of Medical Immunology, Medical University of Gdansk, Gdansk, Poland
| | - Maria Constantinou
- Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland
| | - Robert Śmigiel
- Department of Pediatrics, Division of Pediatrics and Rare Disorders, Wroclaw Medical University, Warsaw, Poland
| | - Jolanta Wierzba
- Department of Internal and Pediatric Nursing, Medical University of Gdansk, Gdansk, Poland
| | - Krystyna Wyka
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
| | - Anna Wędrychowicz
- Polish-American Pediatric Institute, Jagiellonian University Collegium Medicum, Department of Pediatric and Adolescent Endocrinology, Cracow, Poland
| | - Anna Jakubiuk-Tomaszuk
- Department of Pediatric Neurology and Rehabilitation, Medical University of Bialystok, Białystok, Poland
| | - Edyta Budzynska
- Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland
| | - Malgorzata Piotrowicz
- Department of Genetics, Polish Mother’s Memorial Hospital—Research Institute, Lodz, Poland
| | - Beata S. Lipska-Ziętkiewicz
- Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Kaczorowska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Agata Cieślikowska
- Department of Medical Genetics, Children’s Memorial Health Institute, Warsaw, Poland
| | | | - Jolanta Fijak-Moskal
- Outpatient Genetic Clinic, University Children’s Hospital of Cracow, Cracow, Poland
| | - Monika Kugaudo
- Department of Children and Adolescent Psychiatry, University Clinical Center, Pediatric Teaching Clinical Hospital Warsaw, Warsaw, Poland
| | | | - Agnieszka Szadkowska
- Department of Pediatrics, Diabetology, Endocrinology and Nephrology, Medical University of Lodz, Lodz, Poland
| | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland
| | - Maciej Niedźwiecki
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Trzonkowski
- Department of Medical Immunology, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Młynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
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Bohîlţea RE, Cîrstoiu MM, Nedelea FM, Turcan N, Georgescu TA, Munteanu O, Baroş A, Istrate-Ofiţeru AM, Berceanu C. Case report of a novel phenotype in 18q deletion syndrome. ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY 2021; 61:905-910. [PMID: 33817732 PMCID: PMC8112787 DOI: 10.47162/rjme.61.3.29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The latest decades are characterized by an enormous progression in the field of human genetics. In consequences, for various phenotypic manifestations, genetic testing could identify a specific underlying cause. An estimated incidence for all types of 18q deletions is one in 55 000 births predominant on females. About 94% of cases with 18q deletion syndrome appearance are de novo, and the remaining 6% are the inherited from a parent carrying a balanced chromosomal translocation. We present the case of a 35-year-old female who was admitted in our Unit for a second ultrasound opinion after being diagnosed at the second trimester scan at gestational age of 21 weeks of pregnancy with multiple brain and heart malformations, having the recommendation for fetal magnetic resonance imaging (MRI). Further investigations included genetic analysis and pathological examination. Major malformations diagnosed and confirmed were agenesis of the corpus callosum, ventriculomegaly with dilated fourth ventricle, partial agenesis of vermis, bilateral anophthalmia with wide nasal base and left cleft lip. Additional, cardiac malformation, with an important ventricular septal defect and overriding aorta were noted. The results of the microarray analysis showed an abnormal fetal karyotype with a loss of 30.5 basis identified in the long arm of chromosome 18. Although most of the cases of 18q deletion are sporadically or de novo, could be cases where the possible existing syndromes can be inherited from a healthy or mild affected parent. Therefore, in order to establish the recurrence risk, parental karyotypes are recommended.
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Affiliation(s)
- Roxana Elena Bohîlţea
- Department of Anatomy, Department of Pathology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania; ,
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Cody JD. The Consequences of Abnormal Gene Dosage: Lessons from Chromosome 18. Trends Genet 2020; 36:764-776. [PMID: 32660784 DOI: 10.1016/j.tig.2020.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022]
Abstract
Accurate interpretation of genomic copy number variation (CNV) remains a challenge and has important consequences for both congenital and late-onset disease. Hemizygosity dosage characterization of the genes on chromosome 18 reveals a spectrum of outcomes ranging from no clinical effect, to risk factors for disease, to both low- and high-penetrance disease. These data are important for accurate and predictive clinical management. Additionally, the potential mechanisms of reduced penetrance due to dosage compensation are discussed as a key to understanding avenues for potential treatment. This review describes the chromosome 18 findings, and discusses the molecular mechanisms that allow haploinsufficiency, reduced penetrance, and dosage compensation.
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Affiliation(s)
- Jannine DeMars Cody
- Department of Pediatrics, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Chromosome 18 Registry and Research Society, San Antonio, TX 78229, USA.
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Abstract
In 2009, we described the first generation of the chromosome 18 gene dosage maps. This tool included the annotation of each gene as well as each phenotype associated region. The goal of these annotated genetic maps is to provide clinicians with a tool to appreciate the potential clinical impact of a chromosome 18 deletion or duplication. These maps are continually updated with the most recent and relevant data regarding chromosome 18. Over the course of the past decade, there have also been advances in our understanding of the molecular mechanisms underpinning genetic disease. Therefore, we have updated the maps to more accurately reflect this knowledge. Our Gene Dosage Map 2.0 has expanded from the gene and phenotype maps to also include a pair of maps specific to hemizygosity and suprazygosity. Moreover, we have revamped our classification from mechanistic definitions (e.g., haplosufficient, haploinsufficient) to clinically oriented classifications (e.g., risk factor, conditional, low penetrance, causal). This creates a map with gradient of classifications that more accurately represents the spectrum between the two poles of pathogenic and benign. While the data included in this manuscript are specific to chromosome 18, they may serve as a clinically relevant model that can be applied to the rest of the genome.
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Cody JD, Hasi-Zogaj M, Heard P, Hill A, Rupert D, Sebold C, Soileau B, Hale DE. The Chromosome 18 Clinical Resource Center. Mol Genet Genomic Med 2018; 6:416-421. [PMID: 29603904 PMCID: PMC6014460 DOI: 10.1002/mgg3.385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/07/2018] [Accepted: 02/21/2018] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The Chromosome 18 Clinical Research Center has created a pediatrician-friendly virtual resource center for managing patients with chromosome 18 abnormalities. To date, children with rare chromosome abnormalities have been cared for either symptomatically or palliatively as a reaction to the presenting medical problems. As we enter an era of genomic-informed medicine, we can provide children, even those with individually unique chromosome abnormalities, with proactive medical care and management based on the most contemporary data on their specific genomic change. It is problematic for practicing physicians to obtain and use the emerging data on specific genes because this information is derived from diverse sources (e.g., animal studies, case reports, in vitro explorations) and is often published in sources that are not easily accessible in the clinical setting. METHODS The Chromosome 18 Clinical Resource Center remedies this challenging problem by curating and synthesizing the data with clinical implications. The data are collected from our database of over 26 years of natural history and medical data from over 650 individuals with chromosome 18 abnormalities. RESULTS The resulting management guides and video presentations are a first edition of this collated data specifically oriented to guide clinicians toward the optimization of care for each child. CONCLUSION The chromosome 18 data and guides also serve as models for an approach to the management of any individual with a rare chromosome abnormality of which there are over 1,300 born every year in the US alone.
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Affiliation(s)
- Jannine D Cody
- Department of Pediatrics, Chromosome 18 Clinical Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,The Chromosome 18 Registry and Research Society, San Antonio, TX, USA
| | - Minire Hasi-Zogaj
- Department of Pediatrics, Chromosome 18 Clinical Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Patricia Heard
- Department of Pediatrics, Chromosome 18 Clinical Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Annice Hill
- Department of Pediatrics, Chromosome 18 Clinical Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - David Rupert
- Department of Pediatrics, Chromosome 18 Clinical Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Courtney Sebold
- Department of Pediatrics, Chromosome 18 Clinical Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Bridgette Soileau
- Department of Pediatrics, Chromosome 18 Clinical Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Daniel E Hale
- The Chromosome 18 Registry and Research Society, San Antonio, TX, USA.,Department of Pediatrics, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
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Tassano E, Severino M, Rosina S, Papa R, Tortora D, Gimelli G, Cuoco C, Picco P. Interstitial de novo 18q22.3q23 deletion: clinical, neuroradiological and molecular characterization of a new case and review of the literature. Mol Cytogenet 2016; 9:78. [PMID: 27766118 PMCID: PMC5057431 DOI: 10.1186/s13039-016-0285-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/22/2016] [Indexed: 11/25/2022] Open
Abstract
Background Deletions of the long arm of chromosome 18 cause a common autosomal syndrome clinically characterized by a protean clinical phenotype. Case presentation We report on a 16-month-old male infant affected by fever attacks apparently unrelated with any infectious or inflammatory symptoms, growth retardation, bilateral vertical talus, congenital aural atresia, dysmorphisms, mild psychomotor delay, and peculiar neuroradiological features. Array-CGH analysis revealed one of the smallest 18q22.3q23 interstitial deletions involving five genes: TSHZ1, ZNF516, ZNF236, MBP, and GALR1. Conclusions Herein we focus on previously unreported heralding symptoms and neuroradiological abnormalities which enlarge the spectrum of 18q deletion syndrome demonstrating that a small deletion can determine a complex phenotype.
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Affiliation(s)
- Elisa Tassano
- Laboratorio di Citogenetica, Istituto Giannina Gaslini, L.go G.Gaslini 5, 16147 Genoa, Italy
| | | | | | | | | | - Giorgio Gimelli
- Laboratorio di Citogenetica, Istituto Giannina Gaslini, L.go G.Gaslini 5, 16147 Genoa, Italy
| | - Cristina Cuoco
- Laboratorio di Citogenetica, Istituto Giannina Gaslini, L.go G.Gaslini 5, 16147 Genoa, Italy
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Breakpoints and deleted genes identification of ring chromosome 18 in a Chinese girl by whole-genome low-coverage sequencing: a case report study. BMC MEDICAL GENETICS 2016; 17:49. [PMID: 27448395 PMCID: PMC4957311 DOI: 10.1186/s12881-016-0307-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 06/14/2016] [Indexed: 11/10/2022]
Abstract
Background Ring chromosome 18 [r(18)] is formed by 18p- and 18q- partial deletion and generates a ring chromosome. Loss of critical genes on each arm of chromosome 18 may contribute to the specific phenotype, and the clinical spectrum varieties may heavily depend on the extent of the genomic deletion. The aim of this study is to identify the detailed breakpoints location and the deleted genes result from the r18. Case presentation Here we describe a detailed diagnosis of a seven-year-old Chinese girl with a ring chromosome 18 mutation by a high-throughput whole-genome low-coverage sequencing approach without karyotyping and other cytogenetic analysis. This method revealed two fragment heterozygous deletions of 18p and 18q, and further localized the detailed breakpoint sites and fusion, as well as the deleted genes. Conclusions To our knowledge, this is the first report of a ring chromosome 18 patient in China analyzed by whole-genome low-coverage sequencing approach. Detailed breakpoints location and deleted genes identification help to estimate the risk of the disease in the future. The data and analysis here demonstrated the feasibility of next-generation sequencing technologies for chromosome structure variation including ring chromosome in an efficient and cost effective way. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0307-1) contains supplementary material, which is available to authorized users.
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Siu WK, Lam CW, Mak CM, Lau ETK, Tang MHY, Tang WF, Poon-Mak RSM, Lee CC, Hung SF, Leung PWL, Kwong KL, Yau EKC, Ng GSF, Fong NC, Chan KY. Diagnostic yield of array CGH in patients with autism spectrum disorder in Hong Kong. Clin Transl Med 2016; 5:18. [PMID: 27271878 PMCID: PMC4896892 DOI: 10.1186/s40169-016-0098-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/04/2016] [Indexed: 11/25/2022] Open
Abstract
Background Chromosomal microarray offers superior sensitivity for identification of submicroscopic copy number variants (CNV) and it is advocated to be the first tier genetic testing for patients with autism spectrum disorder (ASD). In this regard, diagnostic yield of array comparative genomic hybridization (CGH) for ASD patients is determined in a cohort of Chinese patients in Hong Kong. Methods A combined adult and paediatric cohort of 68 Chinese ASD patients (41 patients in adult group and 27 patients in paediatric group). The genomic DNA extracted from blood samples were analysed by array CGH using NimbleGen CGX-135K oligonucleotide array. Results We identified 15 CNV and eight of them were clinically significant. The overall diagnostic yield was 11.8 %. Five clinically significant CNV were detected in the adult group and three were in the paediatric group, providing diagnostic yields of 12.2 and 11.1 % respectively. The most frequently detected CNV was 16p13.11 duplications which were present in 4 patients (5.9 % of the cohort). Conclusions In this study, a satisfactory diagnostic yield of array CGH was demonstrated in a Chinese ASD patient cohort which supported the clinical usefulness of array CGH as the first line testing of ASD in Hong Kong. Electronic supplementary material The online version of this article (doi:10.1186/s40169-016-0098-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wai-Kwan Siu
- Department of Pathology, The University of Hong Kong, 102 Pokfulam Road, Hong Kong, China.,Kowloon West Cluster Laboratory Genetics Service, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, 102 Pokfulam Road, Hong Kong, China.
| | - Chloe Miu Mak
- Kowloon West Cluster Laboratory Genetics Service, Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Elizabeth Tak-Kwong Lau
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Mary Hoi-Yin Tang
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Wing-Fai Tang
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | | | - Chi-Chiu Lee
- Department of Psychiatry, Kwai Chung Hospital, Hong Kong, China
| | - Se-Fong Hung
- Department of Psychiatry, Kwai Chung Hospital, Hong Kong, China
| | | | - Karen Ling Kwong
- Department of Paediatrics and Adolescent Medicine, Tuen Mun Hospital, Hong Kong, China
| | - Eric Kin-Cheong Yau
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Grace Sui-Fun Ng
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Nai-Chung Fong
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Kwok-Yin Chan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
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13
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Kontodiou M, Daskalakis G, Vetro A, Paspaliaris V, Papaioannou G, Dagklis T, Tsakiridis I, Ziegler M, Liehr T, Thomaidis L, Papoulidis I, Manolakos E. Complex Rearrangement Involving Three Chromosomes, Four Breakpoints and a 2.7-Mb Deletion in the 18q Segment Observed in a Girl with Mild Learning Difficulties. Cytogenet Genome Res 2015; 147:118-23. [PMID: 26681178 DOI: 10.1159/000442583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2015] [Indexed: 11/19/2022] Open
Abstract
Complex chromosomal rearrangements (CCRs) are balanced or unbalanced structural rearrangements involving 3 or more cytogenetic break events on 2 or more different chromosomes. Here, we report a 7-year-old girl referred to our unit because of mild dysmorphic facial features, mild learning difficulties together with very mild mental retardation. Standard cytogenetic banding analysis revealed a de novo CCR involving chromosomes 1, 2 and 18. Further molecular investigation with aCGH revealed a cryptic interstitial deletion of 2.7 Mb in 18q22.1, which does not elicit a significant clinical phenotype. FISH was performed to confirm both molecular and cytogenetic results.
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Affiliation(s)
- Maria Kontodiou
- Access to Genome - ATG P.C., Laboratory of Genetics, Thessaloniki, Greece
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14
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Rittinger O, Krabichler B, Kronberger G, Kotzot D. Clinical, cytogenetic, and molecular findings in a patient with a 46,XX,del(18)(q22)/46,XX,idic(18)(q22) karyotype. Eur J Med Genet 2015; 58:603-7. [PMID: 26417856 DOI: 10.1016/j.ejmg.2015.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/16/2015] [Accepted: 09/23/2015] [Indexed: 11/30/2022]
Abstract
Pseudoisodicentric or asymmetrical dicentric chromosomes 18 are rare findings in clinical cytogenetics. So far, only 8 patients with breakpoints in 18q have been reported and in none of them breakpoints were narrowed down to the molecular level. Here, we describe a 17 months old girl with a perimembranous ventricular septal defect, cleft palate, and minor dysmorphism including hypertelorism, flat nose, frontal bossing and low set ears as well as mosaicism for a cell line with a pseudoisodicentric chromosome 18q and a second cell line with a terminal deletion of 11 Mb in 18q22.2→qter. SNP-array investigation revealed a symmetric breakpoint in 18q22.2 and most likely postzygotic formation from the maternal chromosome 18. Clinical findings in all patients reported so far as well as in the patient presented here were in part overlapping with the clinical phenotypes of trisomy 18 and partial monosomy 18q.
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Affiliation(s)
- Olaf Rittinger
- Department of Pediatrics, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Birgit Krabichler
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriela Kronberger
- Department of Pediatrics, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Dieter Kotzot
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
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15
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Hasi-Zogaj M, Sebold C, Heard P, Carter E, Soileau B, Hill A, Rupert D, Perry B, Atkinson S, O'Donnell L, Gelfond J, Lancaster J, Fox PT, Hale DE, Cody JD. A review of 18p deletions. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2015; 169:251-64. [PMID: 26250845 DOI: 10.1002/ajmg.c.31445] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since 18p- was first described in 1963, much progress has been made in our understanding of this classic deletion condition. We have been able to establish a fairly complete picture of the phenotype when the deletion breakpoint occurs at the centromere, and we are working to establish the phenotypic effects when each gene on 18p is hemizygous. Our aim is to provide genotype-specific anticipatory guidance and recommendations to families with an 18p- diagnosis. In addition, establishing the molecular underpinnings of the condition will potentially suggest targets for molecular treatments. Thus, the next step is to establish the precise effects of specific gene deletions. As we look forward to deepening our understanding of 18p-, our focus will continue to be on the establishment of robust genotype-phenotype correlations and the penetrance of these phenotypes. We will continue to follow our 18p- cohort closely as they age to determine the presence or absence of some of these diagnoses, including spinocerebellar ataxia (SCA), facioscapulohumeral muscular dystrophy (FSHD), and dystonia. We will also continue to refine the critical regions for other phenotypes as we enroll additional (hopefully informative) participants into the research study and as the mechanisms of the genes in these regions are elucidated. Mouse models will also be developed to further our understanding of the effects of hemizygosity as well as to serve as models for treatment development.
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16
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Cody JD, Sebold C, Heard P, Carter E, Soileau B, Hasi-Zogaj M, Hill A, Rupert D, Perry B, O'Donnell L, Gelfond J, Lancaster J, Fox PT, Hale DE. Consequences of chromsome18q deletions. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2015; 169:265-80. [PMID: 26235940 DOI: 10.1002/ajmg.c.31446] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 06/28/2015] [Indexed: 11/11/2022]
Abstract
Providing clinically relevant prognoses and treatment information for people with a chromsome18q deletion is particularly challenging because every unrelated person has a unique region of hemizygosity. The hemizygous region can involve almost any region of 18q including between 1 and 101 genes (30 Mb of DNA). Most individuals have terminal deletions, but in our cohort of over 350 individuals 23% have interstitial deletions. Because of this heterogeneity, we take a gene by gene approach to understanding the clinical consequences. There are 196 genes on 18q. We classified 133 of them as dosage insensitive, 15 (8%) as dosage sensitive leading to haploinsufficiency while another 10 (5%) have effects that are conditionally haploinsufficient and are dependent on another factor, genetic or environmental in order to cause an abnormal phenotype. Thirty-seven genes (19%) have insufficient information to classify their dosage effect. Phenotypes attributed to single genes include: congenital heart disease, minor bone morphology changes, central nervous system dysmyelination, expressive speech delay, vesicouretreral reflux, polyposis, Pitt-Hopkins syndrome, intellectual disability, executive function impairment, male infertility, aural atresia, and high frequency sensorineural hearing loss. Additionally, identified critical regions for other phenotypes include: adolescent idiopathic scoliosis and pectus excavatum, Virchow-Robin perivascular spaces, small corpus callosum, strabismus, atopic disorders, mood disorder, IgA deficiency, nystagmus, congenital heart disease, kidney malformation, vertical talus, CNS dysmyelination growth hormone deficiency and cleft palate. Together these findings make it increasingly feasible to compile an individualized syndrome description based on each person's individuated genotype. Future work will focus on understanding molecular mechanisms leading to treatment.
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17
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Guilherme RS, Hermetz KE, Varela PT, Perez ABA, Meloni VA, Rudd MK, Kulikowski LD, Melaragno MI. Terminal 18q deletions are stabilized by neotelomeres. Mol Cytogenet 2015; 8:32. [PMID: 25969696 PMCID: PMC4427916 DOI: 10.1186/s13039-015-0135-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/14/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND All human chromosomes are capped by tandem repeat (TTAGGG)n sequences that protect them against end-to-end fusion and are essential to chromosomal replication and integrity. Therefore, after a chromosomal breakage, the deleted chromosomes must be stabilized by retaining the telomere or acquiring a new cap, by telomere healing or telomere capture. There are few reports with molecular approaches on the mechanisms involved in stabilization of 18q terminal deletions. RESULTS In this study we analyzed nine patients with 18q terminal deletion identified by G-banding and genomic array. FISH using PNA probe revealed telomeric signals in all deleted chromosomes tested. We fine-mapped breakpoints with customized arrays and sequenced six terminal deletion junctions. In all six deleted chromosomes sequenced, telomeric sequences were found directly attached to the breakpoints. Little or no microhomology was found at the breakpoints and none of the breaks sequenced were located in low copy repeat (LCR) regions, though repetitive elements were found around the breakpoints in five patients. One patient presented a more complex rearrangement with two deleted segments and an addition of 17 base pairs (bp). CONCLUSIONS We found that all six deleted chromosomes sequenced were probably stabilized by the healing mechanism leading to a neotelomere formation.
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Affiliation(s)
- Roberta Santos Guilherme
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP 04023-900, São Paulo, Brazil
| | - Karen E Hermetz
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street Northeast, GA 30322, Atlanta, USA
| | - Patrícia Teixeira Varela
- Department of Biophysics, Universidade Federal de São Paulo, Rua Três de Maio 100, CEP 04023-900, São Paulo, Brazil
| | - Ana Beatriz Alvarez Perez
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP 04023-900, São Paulo, Brazil
| | - Vera Ayres Meloni
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP 04023-900, São Paulo, Brazil
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street Northeast, GA 30322, Atlanta, USA
| | - Leslie Domenici Kulikowski
- Department of Pathology, Laboratório de Citogenômica, Universidade de São Paulo, Avenida Dr. Enéas Carvalho de Aguiar 255, CEP 05403-000, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, CEP 04023-900, São Paulo, Brazil
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18
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Abstract
OBJECTIVE The objective of this study was to characterize hearing loss in individuals with deletions of distal chromsome18q and to identify the smallest region of overlap of their deletions, thereby identifying potential causative genes. STUDY DESIGN The clinical data were collected via a retrospective case study. Molecular data were obtained via high-resolution chromosome microarray analysis. SETTING The study was conducted as a component of the ongoing research protocols at the Chromosome 18 Clinical Research Center at the University of Texas Health Science Center at San Antonio. PATIENTS Thirty-eight participants with a deletion of the distal portion of the long arm of chromosome 18 were recruited to this study. INTERVENTIONS The participants underwent an otologic examination as well as a basic audiometry evaluation. Blood samples were obtained, and high-resolution chromosome microarray analysis was performed. MAIN OUTCOMES MEASURES Pure tone averages and speech discrimination scores were determined for each participant. The region of hemizygosity for each participant was determined to within 2 Kb each of their breakpoints. RESULTS Twenty-four participants (63%) had high-frequency hearing loss, similar to the pattern seen in presbycusis. Comparison of microarray results allowed identification of eight genes, including the candidate gene for dysmyelination (MBP). CONCLUSION Individuals with a deletion of a 2.8 Mb region of 18q23 have a high probability (83%) of high-frequency sensorineural hearing loss.
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Sebold C, Soileau B, Heard P, Carter E, O'Donnell L, Hale DE, Cody JD. Whole arm deletions of 18p: medical and developmental effects. Am J Med Genet A 2015; 167A:313-23. [PMID: 25586871 DOI: 10.1002/ajmg.a.36880] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 10/01/2014] [Indexed: 11/07/2022]
Abstract
Deletions of the short arm of chromosome 18 have been well-described in case reports. However, the utility of these descriptions in clinical practice is limited by varied and imprecise breakpoints. As we work to establish genotype-phenotype correlations for 18p-, it is critical to have accurate and complete clinical descriptions of individuals with differing breakpoints. In addition, the developmental profile of 18p- has not been well-delineated. We undertook a thorough review of the medical histories of 31 individuals with 18p- and a breakpoint in the centromeric region. We collected developmental data using mailed surveys and questionnaires. The most common findings included neonatal complications; cardiac anomalies; hypotonia; MRI abnormalities; endocrine dysfunction; strabismus; ptosis; and refractive errors. Less common features included holoprosencephaly and its microforms; hearing loss; and orthopedic anomalies. The developmental effects of the deletion appear to be less severe than reported in the literature, as average IQ scores were in the range of borderline intellectual functioning. Based on responses to standardized questionnaires, it appears this population has marked difficulty with activities of daily living, though several young adults were able to live independent of their parents. This manuscript represents the most comprehensive description of a cohort of 18p- individuals with identical breakpoints. Despite identical breakpoints, a great deal of phenotype variability remained among this population, suggesting that many of the genes on 18p- cause low-penetrance phenotypes when present in a hemizygous state. Future efforts will focus on the clinical description of individuals with more distal breakpoints and the identification of critical regions and candidate genes.
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Affiliation(s)
- Courtney Sebold
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas
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20
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Córdova-Fletes C, Sáinz-González E, Avendaño-Gálvez RI, Ramírez-Velazco A, Rivera H, Ortiz-López R, Arámbula-Meraz E, Picos-Cárdenas VJ. De novo dir dup/del of 18q characterized by SNP arrays and FISH in a girl child with mixed phenotypes. J Genet 2015; 93:869-73. [PMID: 25572250 DOI: 10.1007/s12041-014-0459-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Carlos Córdova-Fletes
- Laboratorio de Citogenomica y Microarreglos, Departamento de Bioquimica y Medicina Molecular, Facultad de Medicina, Universidad Autonoma de Nuevo Leon, Monterrey, Nuevo Leon 64460, Mexico.
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21
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Adults with Chromosome 18 Abnormalities. J Genet Couns 2014; 24:663-74. [PMID: 25403900 DOI: 10.1007/s10897-014-9793-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/06/2014] [Indexed: 10/24/2022]
Abstract
The identification of an underlying chromosome abnormality frequently marks the endpoint of a diagnostic odyssey. However, families are frequently left with more questions than answers as they consider their child's future. In the case of rare chromosome conditions, a lack of longitudinal data often makes it difficult to provide anticipatory guidance to these families. The objective of this study is to describe the lifespan, educational attainment, living situation, and behavioral phenotype of adults with chromosome 18 abnormalities. The Chromosome 18 Clinical Research Center has enrolled 483 individuals with one of the following conditions: 18q-, 18p-, Tetrasomy 18p, and Ring 18. As a part of the ongoing longitudinal study, we collect data on living arrangements, educational level attained, and employment status as well as data on executive functioning and behavioral skills on an annual basis. Within our cohort, 28 of the 483 participants have died, the majority of whom have deletions encompassing the TCF4 gene or who have unbalanced rearrangement involving other chromosomes. Data regarding the cause of and age at death are presented. We also report on the living situation, educational attainment, and behavioral phenotype of the 151 participants over the age of 18. In general, educational level is higher for people with all these conditions than implied by the early literature, including some that received post-high school education. In addition, some individuals are able to live independently, though at this point they represent a minority of patients. Data on executive function and behavioral phenotype are also presented. Taken together, these data provide insight into the long-term outcome for individuals with a chromosome 18 condition. This information is critical in counseling families on the range of potential outcomes for their child.
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22
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Carter E, Heard P, Hasi M, Soileau B, Sebold C, Hale DE, Cody JD. Ring 18 molecular assessment and clinical consequences. Am J Med Genet A 2014; 167A:54-63. [PMID: 25339348 DOI: 10.1002/ajmg.a.36822] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 09/12/2014] [Indexed: 12/23/2022]
Abstract
Ring chromosome 18 is a rare condition which has predominantly been described by case reports and small case series. We assessed a cohort of 30 individuals with ring 18 using both microarray comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). We determined that each participant had a unique combination of hemizygosity for the p and q arms. Four ring chromosomes had no detectable deletion of one of the chromosome arms using aCGH. However, two of these ring chromosomes had telomeric sequences detected using FISH. These data confirm the importance of molecular and cytogenetic analysis to determine both chromosome content and morphology. We failed to find dramatic changes in mosaicism percentage between cytogenetic measurements made at the time of diagnosis and those made years later at the time of this study, demonstrating that dynamic ring mosaicism is unlikely to be a major cause of phenotypic variability in the ring 18 population. Lastly, we present data on the clinical features present in our cohort, though the extreme genotypic variability makes it impossible to draw direct genotype-phenotype correlations. Future work will focus on determining the role of specific hemizygous genes in order to create individualized projections of the effect of each person's specific ring 18 compliment.
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Affiliation(s)
- Erika Carter
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, Texas
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23
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Oliveira MM, Meloni VA, Canonaco RS, Takeno SS, Bortolai A, de Mello CB, de Lima FT, Melaragno MI. Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome in an adolescent with complex chromosomal rearrangement and intellectual disability. Am J Med Genet A 2014; 164A:2685-8. [PMID: 25081192 DOI: 10.1002/ajmg.a.36690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/27/2014] [Indexed: 01/02/2023]
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24
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Perry BP, Cody JD. Otologic characteristics of individuals with deletions of distal 18q. Laryngoscope 2014; 124:2606-9. [PMID: 24912803 DOI: 10.1002/lary.24769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/21/2014] [Accepted: 05/12/2014] [Indexed: 11/09/2022]
Abstract
OBJECTIVES/HYPOTHESIS To fully describe the otologic features seen in individuals with deletions of the distal long arm of chromosome 18 (distal 18q-). STUDY DESIGN Cross-sectional/observational. METHODS More than 200 individuals with deletions of the long arm of chromosome 18 underwent a complete otologic and audiologic examination. In addition, chromosome microarray analysis to determine the chromosome copy number was completed for all participants. Overall, 113 subjects had clinical and audiological data to be reported here. RESULTS Sixty-six percent of this population had aural stenosis or atresia. No subject had microtia. In the 53 individuals for whom serial data was available, enlargement of ear canal diameter was seen in 48% of ears with stenosis, examined over time. Abnormalities of the palate were seen in nearly 18% of patients and included complete or incomplete clefts of the palate, submucous clefts, and velopharyngeal insufficiency. A conductive hearing impairment was identified in 112 ears (49.5%), and sensorineural hearing loss was identified in 28%. Eustachian tube dysfunction was common and found in 78% of ears examined. CONCLUSIONS The otologic phenotype varies widely among individuals with distal 18q-. External auditory canal stenosis without microtia is a hallmark of the disease. Hearing impairment is also very common, with both sensorineural losses and conductive losses contributing to morbidity. Moreover, the critical region for sensorineural hearing loss will aid in the identification of the gene responsible for this aspect of the distal 18q- phenotype. LEVEL OF EVIDENCE 4.
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25
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Hermetz KE, Newman S, Conneely KN, Martin CL, Ballif BC, Shaffer LG, Cody JD, Rudd MK. Large inverted duplications in the human genome form via a fold-back mechanism. PLoS Genet 2014; 10:e1004139. [PMID: 24497845 PMCID: PMC3907307 DOI: 10.1371/journal.pgen.1004139] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/09/2013] [Indexed: 11/27/2022] Open
Abstract
Inverted duplications are a common type of copy number variation (CNV) in germline and somatic genomes. Large duplications that include many genes can lead to both neurodevelopmental phenotypes in children and gene amplifications in tumors. There are several models for inverted duplication formation, most of which include a dicentric chromosome intermediate followed by breakage-fusion-bridge (BFB) cycles, but the mechanisms that give rise to the inverted dicentric chromosome in most inverted duplications remain unknown. Here we have combined high-resolution array CGH, custom sequence capture, next-generation sequencing, and long-range PCR to analyze the breakpoints of 50 nonrecurrent inverted duplications in patients with intellectual disability, autism, and congenital anomalies. For half of the rearrangements in our study, we sequenced at least one breakpoint junction. Sequence analysis of breakpoint junctions reveals a normal-copy disomic spacer between inverted and non-inverted copies of the duplication. Further, short inverted sequences are present at the boundary of the disomic spacer and the inverted duplication. These data support a mechanism of inverted duplication formation whereby a chromosome with a double-strand break intrastrand pairs with itself to form a “fold-back” intermediate that, after DNA replication, produces a dicentric inverted chromosome with a disomic spacer corresponding to the site of the fold-back loop. This process can lead to inverted duplications adjacent to terminal deletions, inverted duplications juxtaposed to translocations, and inverted duplication ring chromosomes. Chromosomes with large inverted duplications and terminal deletions cause neurodevelopmental disorders in children. These chromosome rearrangements typically involve hundreds of genes, leading to significant changes in gene dosage. Though inverted duplications adjacent to terminal deletions are a relatively common type of chromosomal imbalance, the DNA repair mechanism responsible for their formation is not known. In this study, we analyze the genomic organization of the largest collection of human inverted duplications. We find a common inverted duplication structure, consistent with a model that requires DNA to fold back and form a dicentric chromosome intermediate. These data provide insight into the formation of nonrecurrent inverted duplications in the human genome.
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Affiliation(s)
- Karen E Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Scott Newman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America ; Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia, United States of America
| | - Christa L Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Blake C Ballif
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Jannine D Cody
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America ; The Chromosome 18 Registry and Research Society, San Antonio, Texas, United States of America
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
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26
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Daviss WB, O'Donnell L, Soileau BT, Heard P, Carter E, Pliszka SR, Gelfond JAL, Hale DE, Cody JD. Mood disorders in individuals with distal 18q deletions. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:879-88. [PMID: 24006251 DOI: 10.1002/ajmg.b.32197] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 08/02/2013] [Indexed: 12/27/2022]
Abstract
We examined 36 participants at least 4 years old with hemizygous distal deletions of the long arm of Chromosome 18 (18q-) for histories of mood disorders and to characterize these disorders clinically. Since each participant had a different region of 18q hemizygosity, our goal was also to identify their common region of hemizygosity associated with mood disorders; thereby identifying candidate causal genes in that region. Lifetime mood and other psychiatric disorders were determined by semi-structured interviews of patients and parents, supplemented by reviews of medical and psychiatric records, and norm-referenced psychological assessment instruments, for psychiatric symptoms, cognitive problems, and adaptive functioning. Sixteen participants were identified with lifetime mood disorders (ages 12-42 years, 71% female, 14 having had unipolar depression and 2 with bipolar disorders). From the group of 20 who did not meet criteria for a mood disorder; a comparison group of 6 participants were identified who were matched for age range and deletion size. Mood-disordered patients had high rates of anxiety (75%) and externalizing behavior disorders (44%), and significant mean differences from comparison patients (P < 0.05), including higher overall and verbal IQs and lower autistic symptoms. A critical region was defined in the mood-disordered group that included a hypothetical gene, C18orf62, and two known genes, ZADH2 and TSHZ1. We conclude that patients having terminal deletions of this critical region of the long arm of Chromosome 18 are highly likely to have mood disorders, which are often comorbid with anxiety and to a lesser extent with externalizing disorders.
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Affiliation(s)
- William B Daviss
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, Texas
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27
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Establishing a reference group for distal 18q-: clinical description and molecular basis. Hum Genet 2013; 133:199-209. [PMID: 24092497 DOI: 10.1007/s00439-013-1364-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/18/2013] [Indexed: 12/16/2022]
Abstract
Although constitutional chromosome abnormalities have been recognized since the 1960s, clinical characterization and development of treatment options have been hampered by their obvious genetic complexity and relative rarity. Additionally, deletions of 18q are particularly heterogeneous, with no two people having the same breakpoints. We identified 16 individuals with deletions that, despite unique breakpoints, encompass the same set of genes within a 17.6-Mb region. This group represents the most genotypically similar group yet identified with distal 18q deletions. As the deletion is of average size when compared with other 18q deletions, this group can serve as a reference point for the clinical and molecular description of this condition. We performed a thorough medical record review as well as a series of clinical evaluations on 14 of the 16 individuals. Common functional findings included developmental delays, hypotonia, growth hormone deficiency, and hearing loss. Structural anomalies included foot anomalies, ear canal atresia/stenosis, and hypospadias. The majority of individuals performed within the low normal range of cognitive ability but had more serious deficits in adaptive abilities. Of interest, the hemizygous region contains 38 known genes, 26 of which are sufficiently understood to tentatively determine dosage sensitivity. Published data suggest that 20 are unlikely to cause an abnormal phenotype in the hemizygous state and five are likely to be dosage sensitive: TNX3, NETO1, ZNF407, TSHZ1, and NFATC. A sixth gene, ATP9B, may be conditionally dosage sensitive. Not all distal 18q- phenotypes can be attributed to these six genes; however, this is an important advance in the molecular characterization of 18q deletions.
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Spreiz A, Guilherme RS, Castellan C, Green A, Rittinger O, Wellek B, Utermann B, Erdel M, Fauth C, Haberlandt E, Kim CA, Kulikowski LD, Meloni VA, Utermann G, Zschocke J, Melaragno MI, Kotzot D. Single-nucleotide polymorphism array-based characterization of ring chromosome 18. J Pediatr 2013; 163:1174-8.e3. [PMID: 23876976 DOI: 10.1016/j.jpeds.2013.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 04/23/2013] [Accepted: 06/06/2013] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To study genotype-phenotype correlation of ring chromosome 18 [r(18)] in 9 patients with 46,XN karyotype. STUDY DESIGN In 9 patients with a de novo 46,XN,r(18) karyotype (7 females, 2 males), we performed high-resolution single-nucleotide polymorphism array analysis (Illumina Human Omni1-QuadV1 array in 6 patients, Affymetrix 6.0 array in 3 patients), investigation of parental origin, and genotype-phenotype correlation. RESULTS No breakpoint was recurrent. Single metaphases with loss of the ring, double rings, or secondarily rearranged rings were found in some cases, but true mosaicism was present in none of these cases. In 3 patients, additional duplications in 18p (of 1.4 Mb, 2 Mb, and 5.8 Mb) were detected. In 1 patient, an additional deletion of 472 kb in Xp22.33, including the SHOX gene, was found. Parental origin of r(18) was maternal in 2 patients and paternal in 4 patients, and formation was most likely meiotic. Karyotype was normal in all investigated parents (n = 15). At birth, mean maternal age was 30 years (n = 9) and mean paternal age was 34.4 years (n = 9). CONCLUSION Genotype-phenotype correlation revealed extensive clinical variability but no characteristic r(18) phenotype. Severity of clinical signs were generally correlated with the size of the deletion. Patients with large deletions in 18p and small deletions in 18q exhibited mainly symptoms related to 18p-, whereas those with large deletions in 18q and small deletions in 18p had symptoms of 18q-.
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Affiliation(s)
- Ana Spreiz
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
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Combined deletion 18q22.2 and duplication/triplication 18q22.1 causes microcephaly, mental retardation and leukencephalopathy. Gene 2013; 523:92-8. [DOI: 10.1016/j.gene.2013.03.078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/05/2013] [Accepted: 03/15/2013] [Indexed: 11/23/2022]
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30
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Müller P, Ramel C, Franke K, Riedel S, Junge A, Reichenbach H. Autoimmunerkrankungen, mentale Retardierung und Dysmorphien. Monatsschr Kinderheilkd 2012. [DOI: 10.1007/s00112-012-2701-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Malan V, Romana S. Diagnostic des anomalies chromosomiques par CGH array en pathologie constitutionnelle : la fin du caryotype en première intention. Arch Pediatr 2012; 19:437-42. [DOI: 10.1016/j.arcped.2012.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/16/2012] [Accepted: 01/20/2012] [Indexed: 02/01/2023]
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Margarit E, Morales C, Rodríguez-Revenga L, Monné R, Badenas C, Soler A, Clusellas N, Mademont I, Sánchez A. Familial 4.8 MB deletion on 18q23 associated with growth hormone insufficiency and phenotypic variability. Am J Med Genet A 2012; 158A:611-6. [PMID: 22302430 DOI: 10.1002/ajmg.a.34221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 05/23/2011] [Indexed: 11/07/2022]
Abstract
The deletion of the long arm of chromosome 18 causes a contiguous gene deletion syndrome with a highly variable phenotype, usually related to the extent of the deleted region. The most commonly reported clinical features include: decreased growth, microcephaly, facial abnormalities, hypotonia, developmental delay, intellectual disability, congenital aural atresia with hearing impairment and limb anomalies. Here we report on a familial terminal deletion of 18q23 region transmitted from a mother to two daughters, resulting in a remarkable phenotypic variability. The deletion was first detected by conventional cytogenetic analysis in one daughter and subsequently characterized using fluorescence in situ hybridization (FISH) and array-CGH. FISH analysis using subtelomeric 18p and 18q probes confirmed the 18qter deletion in the three patients, and FISH with a whole chromosome painting probe specific for chromosome 18 excluded rearrangements with other chromosomes. Array-CGH analysis allowed us to precisely define the extent of the deletion, which spans 4.8 Mb from 71,236,891 to 76,093,303 genomic positions and includes GALR1 and MBP genes, among others. High-resolution analysis of the deletion, besides a detailed clinical assessment, has provided important data for phenotype-genotype correlation and genetic counseling in this family. Furthermore, this study adds valuable information for phenotype-genotype correlation in 18q- syndrome and might facilitate future search for candidate genes involved in each phenotypic trait.
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Affiliation(s)
- Ester Margarit
- Biochemistry and Molecular Genetics, Hospital Clínic, Barcelona, Spain.
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Abstract
Pitt-Hopkins syndrome (PTHS, MIM #610954) is characterized by severe intellectual disability, typical facial features and tendency to epilepsy, panting-and-holding breathing anomaly, stereotypic movements, constipation, and high myopia. Growth is normal or only mildly retarded, but half of the patients have postnatal microcephaly. Remarkably, congenital malformations are practically nonexistent. The cause of PTHS is de novo haploinsufficiency of the TCF4 gene (MIM *602272) at 18q21.2. Altogether 78 PTHS patients with abnormalities of the TCF4 gene have been published since 2007 when the etiology of PTHS was revealed. In addition, 27 patients with 18q deletion encompassing the TCF4 gene but without given PTHS diagnosis have been published, and thus, the number of reported patients with a TCF4 abnormality exceeds 100. The mutational spectrum includes large chromosomal deletions encompassing the whole TCF4 gene, partial gene deletions, frameshift (including premature stop codon), nonsense, splice site, and missense mutations. So far, almost all patients have a private mutation and only 2 recurrent mutations are known. There is no evident genotype-phenotype correlation. No familial cases have been reported. Diagnosis of PTHS is based on the molecular confirmation of the characteristic clinical features. Recently, a Pitt-Hopkins-like phenotype has been assigned to autosomal recessive mutations of the CNTNAP2 gene at 7q33q36 and the NRXN1 gene at 2p16.3.
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Affiliation(s)
- M Peippo
- Department of Medical Genetics, The Family Federation of Finland, Helsinki, Finland
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Luo Y, Hermetz KE, Jackson JM, Mulle JG, Dodd A, Tsuchiya KD, Ballif BC, Shaffer LG, Cody JD, Ledbetter DH, Martin CL, Rudd MK. Diverse mutational mechanisms cause pathogenic subtelomeric rearrangements. Hum Mol Genet 2011; 20:3769-78. [PMID: 21729882 DOI: 10.1093/hmg/ddr293] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromosome rearrangements are a significant cause of intellectual disability and birth defects. Subtelomeric rearrangements, including deletions, duplications and translocations of chromosome ends, were first discovered over 40 years ago and are now recognized as being responsible for several genetic syndromes. Unlike the deletions and duplications that cause some genomic disorders, subtelomeric rearrangements do not typically have recurrent breakpoints and involve many different chromosome ends. To capture the molecular mechanisms responsible for this heterogeneous class of chromosome abnormality, we coupled high-resolution array CGH with breakpoint junction sequencing of a diverse collection of subtelomeric rearrangements. We analyzed 102 breakpoints corresponding to 78 rearrangements involving 28 chromosome ends. Sequencing 21 breakpoint junctions revealed signatures of non-homologous end-joining, non-allelic homologous recombination between interspersed repeats and DNA replication processes. Thus, subtelomeric rearrangements arise from diverse mutational mechanisms. In addition, we find hotspots of subtelomeric breakage at the end of chromosomes 9q and 22q; these sites may correspond to genomic regions that are particularly susceptible to double-strand breaks. Finally, fine-mapping the smallest subtelomeric rearrangements has narrowed the critical regions for some chromosomal disorders.
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Affiliation(s)
- Yue Luo
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
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35
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Bartels E, Draaken M, Kazmierczak B, Spranger S, Schramm C, Baudisch F, Nöthen MM, Schmiedeke E, Ludwig M, Reutter H. De novo partial trisomy 18p and partial monosomy 18q in a patient with anorectal malformation. Cytogenet Genome Res 2011; 134:243-8. [PMID: 21709416 DOI: 10.1159/000328833] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2011] [Indexed: 01/24/2023] Open
Abstract
Anorectal malformations (ARM) encompass a broad clinical spectrum which ranges from mild anal stenosis to severe anorectal anomalies such as complex cloacal malformations. The overall incidence of ARM is around 1 in every 2,500 live births. Although causative genes for a few syndromic forms have been identified, the molecular genetic background of most ARM remains unknown. The present report describes a patient with a de novo 13.2-Mb deletion of chromosome 18q22.3-qter and a 2.2-Mb de novo duplication of chromosomal region 18pter-p11.32 located at the telomeric end of chromosome 18q. The patient presented with ARM and the typical features of 18q- syndrome (De-Grouchy syndrome). The combination of a partial duplication of the short arm and a partial deletion of the long arm of chromosome 18 has been described in 16 previous cases. However, this is the first report of an association between this complex chromosomal rearrangement and ARM.
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Affiliation(s)
- E Bartels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
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Hasi M, Soileau B, Sebold C, Hill A, Hale DE, O'Donnell L, Cody JD. The role of the TCF4 gene in the phenotype of individuals with 18q segmental deletions. Hum Genet 2011; 130:777-87. [PMID: 21671075 DOI: 10.1007/s00439-011-1020-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 05/25/2011] [Indexed: 11/26/2022]
Abstract
The goal of this study is to define the effects of TCF4 hemizygosity in the context of a larger segmental deletion of chromosome 18q. Our cohort included 37 individuals with deletions of 18q. Twenty-seven had deletions including TCF4 (TCF4 (+/-)); nine had deletions that did not include TCF4 (TCF4 (+/+)); and one individual had a microdeletion that included only the TCF4 gene. We compared phenotypic data from the participants' medical records, survey responses, and in-person evaluations. Features unique to the TCF4 (+/-) individuals included abnormal corpus callosum, short neck, small penis, accessory and wide-spaced nipples, broad or clubbed fingers, and sacral dimple. The developmental data revealed that TCF4 (+/+) individuals were only moderately developmentally delayed while TCF4 (+/-) individuals failed to reach developmental milestones beyond those typically acquired by 12 months of age. TCF4 hemizygosity also conferred an increased risk of early death principally due to aspiration-related complications. Hemizygosity for TCF4 confers a significant impact primarily with regard to cognitive and motor development, resulting in a very different prognosis for individuals hemizygous for TCF4 when compared to individuals hemizygous for other regions of distal 18q.
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Affiliation(s)
- Minire Hasi
- Department of Pediatrics, UT Health Science Center, 7703 Floyd Curl Dive, San Antonio, TX 78229, USA
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Vásquez-Velásquez AI, Torres-Flores J, Leal CA, Rivera H. Apparent neotelomere in a 46,X,del(X)(qter→p11.2:)/46,X,rea(X)(qter→p11.2::q21.2→qter) novel mosaicism: review of 34 females with a recombinant-like dup(Xq) chromosome. Genet Test Mol Biomarkers 2011; 15:727-31. [PMID: 21651320 DOI: 10.1089/gtmb.2011.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A 26-year-old woman with secondary amenorrhea and turneroid stigmata was found to have a 46,X,rea(X)(qter→p11.2::q21.2→qter)/46,X,del(X)(qter→p11.2:) mosaicism in 101 G-banded metaphases (71 and 30, respectively). The mother's karyotype was normal (the father was already deceased). A fully skewed inactivation of both abnormal X-chromosomes was documented in RBG-banded metaphases and by means of the HUMARA assay. In addition, the latter revealed that the involved X-chromosome was the paternal one. The patient's secondary amenorrhea and turneroid stigmata can reliably be ascribed to her nearly complete Xp deletion present in all cells. Thus, this observation is consistent with the well-known gradation of ovarian function depending on the Xp deletion size. We assume that the first event was an intrachromosome recombination during paternal meiosis between paralogous sequences at Xp11.2 and Xq21.2, which resulted in a fertilizing rea(X) spermatozoid. Early in embryogenesis, the rea(X) dissociated at the Xp11.2 junction point to originate the del(X), which in turn was healed by the de novo addition of telomeric repeats (the acentric Xq21.2→qter segment was lost in the process). The reverse sequence appears unlikely because it implies that the del(X) chromosome was healed only after it undergone a postzygotic interchromatid recombination and apposite segregation required to obtain the rea(X) clone. The present observation further expands the cytogenetic heterogeneity in Turner syndrome and may represent another instance of a terminal deletion healed by the de novo addition of telomeric repeats.
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Sebold C, Roeder E, Zimmerman M, Soileau B, Heard P, Carter E, Schatz M, White WA, Perry B, Reinker K, O'Donnell L, Lancaster J, Li J, Hasi M, Hill A, Pankratz L, Hale DE, Cody JD. Tetrasomy 18p: report of the molecular and clinical findings of 43 individuals. Am J Med Genet A 2010; 152A:2164-72. [PMID: 20803640 DOI: 10.1002/ajmg.a.33597] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Thus far, the phenotype of tetrasomy 18p has been primarily delineated by published case series and reports. Findings reported in more than 25% of these cases include neonatal feeding problems, growth retardation, microcephaly, strabismus, muscle tone abnormalities, scoliosis/kyphosis, and variants on brain MRI. Developmental delays and cognitive impairment are universally present. The purpose of this study was to more fully describe tetrasomy 18p at both the genotypic and the phenotypic levels. Array CGH was performed on 43 samples from individuals with tetrasomy 18p diagnosed via routine karyotype. The medical records of 42 of these 43 individuals were reviewed. In order to gain additional phenotypic data, 31 individuals with tetrasomy 18p underwent a series of clinical evaluations at the Chromosome 18 Clinical Research Center. Results from the molecular analysis indicated that 42 of 43 samples analyzed had 4 copies of the entire p arm of chromosome 18; one individual was also trisomic for a section of proximal 18q. The results of the medical records review and clinical evaluations expand the phenotypic description of tetrasomy 18p to include neonatal jaundice and respiratory distress; recurrent otitis media; hearing loss; seizures; refractive errors; constipation and gastroesophageal reflux; cryptorchidism; heart defects; and foot anomalies. Additional findings identified in a small number of individuals include hernias, myelomeningocele, kidney defects, short stature, and failure to respond to growth hormone stimulation testing. Additionally, a profile of dysmorphic features is described. Lastly, a series of clinical evaluations to be considered for individuals with tetrasomy 18p is suggested.
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Affiliation(s)
- Courtney Sebold
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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39
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O’Donnell L, Soileau B, Heard P, Carter E, Sebold C, Gelfond J, Hale DE, Cody JD. Genetic determinants of autism in individuals with deletions of 18q. Hum Genet 2010; 128:155-64. [DOI: 10.1007/s00439-010-0839-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 05/11/2010] [Indexed: 11/29/2022]
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Abstract
PURPOSE Microarray technology has revolutionized the field of clinical genetics with the ability to detect very small copy number changes. However, challenges remain in linking genotype with phenotype. Our goal is to enable a clinical geneticist to align the molecular karyotype information from an individual patient with the annotated genomic content, so as to provide a clinical prognosis. METHODS We have combined data regarding copy number variations, microdeletion syndromes, and classical chromosome abnormalities, with the sparse but growing knowledge about the biological role of specific genes to create a genomic map of Chromosome 18 with clinical utility. RESULTS We have created a draft model of such a map, drawing from our long-standing interest in and data regarding the abnormalities of Chromosome 18. CONCLUSION We have taken the first step toward creating a genomic map that can be used by the clinician in counseling and directing preventive or symptomatic care of individuals with Chromosome 18 abnormalities.
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Cody JD, Heard PL, Crandall AC, Carter EM, Li J, Hardies LJ, Lancaster J, Perry B, Stratton RF, Sebold C, Schaub RL, Soileau B, Hill A, Hasi M, Fox PT, Hale DE. Narrowing critical regions and determining penetrance for selected 18q- phenotypes. Am J Med Genet A 2009; 149A:1421-30. [PMID: 19533771 DOI: 10.1002/ajmg.a.32899] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
One of our primary goals is to help families who have a child with an 18q deletion anticipate medical issues in order to optimize their child's medical care. To this end we have narrowed the critical regions for four phenotypic features and determined the penetrance for each of those phenotypes when the critical region for that feature is hemizygous. We completed molecular analysis using oligo-array CGH and clinical assessments on 151 individuals with deletions of 18q and made genotype-phenotype correlations defining or narrowing critical regions. These nested regions, all within 18q22.3 to q23, were for kidney malformations, dysmyelination of the brain, growth hormone stimulation response failure, and aural atresia. The region for dysmyelination and growth hormone stimulation response failure were identical and was narrowed to 1.62 Mb, a region containing five known genes. The region for aural atresia was 2.3 Mb and includes an additional three genes. The region for kidney malformations was 3.21 Mb and includes an additional four genes. Penetrance rates were calculated by comparing the number of individuals hemizygous for a critical region with the phenotype to those without the phenotype. The kidney malformations region was 25% penetrant, the dysmyelination region was 100% penetrant, the growth hormone stimulant response failure region was 90% penetrant with variable expressivity, and the aural atresia region was 78% penetrant. Identification of these critical regions suggest possible candidate genes, while penetrance calculations begin to create a predictive phenotypic description based on genotype.
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Affiliation(s)
- Jannine D Cody
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA.
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