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A pure de novo 16p13.3 duplication and amplification in a patient with femoral hypoplasia, psychomotor retardation, heart defect, and facial dysmorphism-a case report and literature review of the partial 16p13.3 trisomy syndrome. J Appl Genet 2023; 64:125-134. [PMID: 36586055 PMCID: PMC9837002 DOI: 10.1007/s13353-022-00743-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/01/2023]
Abstract
Partial 16p trisomy syndrome is a rare disorder typically characterized by psychomotor retardation, prenatal and postnatal growth deficiency, cleft palate, and facial dysmorphism, with some patients also presenting with heart defects and urogenital anomalies. Pure 16p13.3 duplications usually occur de novo, while those duplications that associate with partial monosomy result rather from parental chromosomal translocations. Due to the large size of the aberrations, the majority of patients are identified by standard chromosome analysis. In all published cases, the minimal-causative duplicated region encompasses the CREBBP gene. Here, we report on the patient presenting with psychomotor retardation, femoral hypoplasia, and some features of the partial 16p trisomy syndrome, who carries a complex de novo terminal 16p13.3 microduplication with an overlapping region of amplification without translocation or associated monosomy. In contrast to the previously reported cases, the duplicated region of the patient does not involve CREBBP and other neighboring genes; still, the observed pattern of dysmorphic features of the index is characteristic of the described syndrome. Based on the animal studies and other published cases, we discuss the possible role of the PDK1 and IGFALS genes in the development of limb anomalies, while IFT140 could contribute both to the observed femoral phenotype and heart abnormalities in the patient. To the best of our knowledge, we present a proband harboring the smallest terminal 16p13.3 duplication of the size below 3 Mb. Therefore, our proband with her detailed phenotypic description may be helpful for clinicians who consult patients with this syndrome.
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Popescu R, Grămescu M, Caba L, Pânzaru MC, Butnariu L, Braha E, Popa S, Rusu C, Cardos G, Zeleniuc M, Martiniuc V, Gug C, Păduraru L, Stamatin M, Diaconu CC, Gorduza EV. A Case of Inherited t(4;10)(q26;q26.2) Chromosomal Translocation Elucidated by Multiple Chromosomal and Molecular Analyses. Case Report and Review of the Literature. Genes (Basel) 2021; 12:genes12121957. [PMID: 34946906 PMCID: PMC8701147 DOI: 10.3390/genes12121957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 01/05/2023] Open
Abstract
We present a complex chromosomal anomaly identified using cytogenetic and molecular methods. The child was diagnosed during the neonatal period with a multiple congenital anomalies syndrome characterized by: flattened occipital region; slight turricephaly; tall and broad forehead; hypertelorism; deep-set eyes; down slanting and short palpebral fissures; epicanthic folds; prominent nose with wide root and bulbous tip; microstomia; micro-retrognathia, large, short philtrum with prominent reliefs; low set, prominent ears; and congenital heart disease. The GTG banding karyotype showed a 46,XY,der(10)(10pter→10q26.2::4q26→4qter) chromosomal formula and his mother presented an apparently balanced reciprocal translocation: 46,XX,t(4;10)(q26;q26.2). The chromosomal anomalies of the child were confirmed by MLPA, and supplementary investigation discovered a quadruplication of the 4q35.2 region. The mother has a triplication of the same chromosomal fragment (4q35.2). Using array-CGH, we described the anomalies completely. Thus, the boy has a 71,057 kb triplication of the 4q26-q35.2 region, a 562 kb microdeletion in the 10q26.3 region, and a 795 kb quadruplication of the 4q35.2 region, while the mother presents a 795 kb triplication of the 4q35.2 region. Analyzing these data, we consider that the boy's phenotype is influenced only by the 4q partial trisomy. We compare our case with similar cases, and we review the literature data.
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Affiliation(s)
- Roxana Popescu
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Mihaela Grămescu
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Lavinia Caba
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
- Correspondence: (L.C.); (C.G.)
| | - Monica-Cristina Pânzaru
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Lăcrămioara Butnariu
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Elena Braha
- “C. I. Parhon” National Institute of Endocrinology, 34-35 Aviatorilor Avenue, 011853 Bucharest, Romania;
| | - Setalia Popa
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Cristina Rusu
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Georgeta Cardos
- Personal Genetics Laboratory Bucharest, 4 Strada Frumoasa Street, 010987 Bucharest, Romania; (G.C.); (M.Z.)
| | - Monica Zeleniuc
- Personal Genetics Laboratory Bucharest, 4 Strada Frumoasa Street, 010987 Bucharest, Romania; (G.C.); (M.Z.)
- Medical Genetics Department, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Avenue, 050474 Bucharest, Romania
| | - Violeta Martiniuc
- Medical Genetics Department, “Cuza-Vodă” Obstetrics and Gynecology Hospital, 34 Cuza Voda Street, 700038 Iasi, Romania;
| | - Cristina Gug
- Microscopic Morphology Department, “Victor Babes” University of Medicine and Pharmacy, 2 Piata Eftimie Murgu, 300041 Timișoara, Romania
- Correspondence: (L.C.); (C.G.)
| | - Luminiţa Păduraru
- Neonatology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (L.P.); (M.S.)
| | - Maria Stamatin
- Neonatology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (L.P.); (M.S.)
| | - Carmen C. Diaconu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 285 Mihai Bravu, 030304 Bucharest, Romania;
| | - Eusebiu Vlad Gorduza
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
- Medical Genetics Department, “Cuza-Vodă” Obstetrics and Gynecology Hospital, 34 Cuza Voda Street, 700038 Iasi, Romania;
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3
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De novo 16p13.3-p12.3 duplication in a child with syndromic developmental delay. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Candelo E, Caicedo G, Mejia L, Pachajoa H. Chromosome 17p13.3 microdeletion syndrome with unaltered PAFAH1B1 gene. NEUROLOGÍA (ENGLISH EDITION) 2019. [DOI: 10.1016/j.nrleng.2018.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Mohan S, Koshy T, Vekatachalam P, Nampoothiri S, Yesodharan D, Gowrishankar K, Kumar J, Ravichandran L, Joseph S, Chandrasekaran A, Paul SFD. Subtelomeric rearrangements in Indian children with idiopathic intellectual disability/developmental delay: Frequency estimation & clinical correlation using fluorescence in situ hybridization (FISH). Indian J Med Res 2017; 144:206-214. [PMID: 27934799 PMCID: PMC5206871 DOI: 10.4103/0971-5916.195031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
Background & objectives: Subtelomeres are prone to deleterious rearrangements owing to their proximity to unique sequences on the one end and telomeric repetitive sequences, which increase their tendency to recombine, on the other end. These subtelomeric rearrangements resulting in segmental aneusomy are reported to contribute to the aetiology of idiopathic intellectual disability/developmental delay (ID/DD). We undertook this study to estimate the frequency of subtelomeric rearrangements in children with ID/DD. Methods: One hundred and twenty seven children with idiopathic ID/DD were tested for subtelomeric rearrangements using karyotyping and FISH. Blood samples were cultured, harvested, fixed and GTG-banded using the standard protocols. Results: Rearrangements involving the subtelomeres were observed in 7.8 per cent of the tested samples. Detection of rearrangements visible at the resolution of the karyotype constituted 2.3 per cent, while those rearrangements detected only with FISH constituted 5.5 per cent. Five deletions and five unbalanced translocations were detected. Analysis of parental samples wherever possible was informative regarding the inheritance of the rearrangement. Interpretation & conclusions: The frequency of subtelomeric rearrangements observed in this study was within the reported range of 0-35 per cent. All abnormal genotypes were clinically correlated. Further analysis with array technologies presents a future prospect. Our results suggest the need to test individuals with ID/DD for subtelomeric rearrangements using sensitive methods such as FISH.
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Affiliation(s)
- Shruthi Mohan
- Department of Human Genetics, Sri Ramachandra University, Porur, India
| | - Teena Koshy
- Department of Human Genetics, Sri Ramachandra University, Porur, India
| | | | - Sheela Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences, Kochi, India
| | - Dhanya Yesodharan
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences, Kochi, India
| | - Kalpana Gowrishankar
- Department of Medical Genetics, CHILDS Trust Medical Research Foundation, Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India
| | - Jeevan Kumar
- Department of Medical Genetics, CHILDS Trust Medical Research Foundation, Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India
| | | | - Santhosh Joseph
- Department of Radiology, Sri Ramachandra University, Porur, India
| | | | - Solomon F D Paul
- Department of Human Genetics, Sri Ramachandra University, Porur, India
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Ciaccio C, Tucci A, Scuvera G, Estienne M, Esposito S, Milani D. 16p13 microduplication without CREBBP involvement: Moving toward a phenotype delineation. Eur J Med Genet 2016; 60:159-162. [PMID: 28007608 DOI: 10.1016/j.ejmg.2016.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 12/18/2022]
Abstract
The short arm of chromosome 16 is one of the less stable regions of our genome, as over 10% of the euchromatic region of 16p is composed of highly complex low copy repeats that are known to be predisposed to rearrangements mediated by non-allelic homologous recombination. The 16p13.3p13.13 molecular region has been defined as the 16p duplication hotspot, and duplications of chromosome 16p13 have recently been confirmed to cause a recognizable syndrome, with CREBBP being the main phenotype-causing gene. To date, only one case report is present in the literature with a 16p13 duplication without CREBBP involvement; we describe here a second analogous case with a not previously reported 16p13.2p13.13 microduplication. This paper allows us to better delineate the clinical features of 16p13 microduplications that do not encompass CREBBP and, concurrently, to narrow the molecular region responsible for congenital heart defects in 16p duplications as well as to propose GRIN2A as a candidate gene for epilepsy.
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Affiliation(s)
- Claudia Ciaccio
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy.
| | - Arianna Tucci
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Giulietta Scuvera
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | | | - Susanna Esposito
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
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7
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Chromosome 17p13.3 microdeletion syndrome with unaltered PAFAH1B1 gene. Neurologia 2016; 34:482-484. [PMID: 27939114 DOI: 10.1016/j.nrl.2016.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 11/23/2022] Open
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8
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Vermeesch JR, Melotte C, Froyen G, Van Vooren S, Dutta B, Maas N, Vermeulen S, Menten B, Speleman F, De Moor B, Van Hummelen P, Marynen P, Fryns JP, Devriendt K. Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2016; 53:413-22. [PMID: 15750031 DOI: 10.1369/jhc.4a6436.2005] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Array CGH (comparative genomic hybridization) enables the identification of chromosomal copy number changes. The availability of clone sets covering the human genome opens the possibility for the widespread use of array CGH for both research and diagnostic purposes. In this manuscript we report on the parameters that were critical for successful implementation of the technology, assess quality criteria, and discuss the potential benefits and pitfalls of the technology for improved pre- and postnatal constitutional genetic diagnosis. We propose to name the genome-wide array CGH “molecular karyotyping,” in analogy with conventional karyotyping that uses staining methods to visualize chromosomes.
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Fontes MIB, Santos AP, Molck MC, Simioni M, Nascimento DLL, Andrade AKM, Rosenberg C, Krepischi ACV, Appenzeller S, Monlleó IL, Gil-da-Silva-Lopes VL. Genotype-phenotype correlation of 16p13.3 terminal duplication and 22q13.33 deletion: Natural history of a patient and review of the literature. Am J Med Genet A 2015; 170:766-72. [PMID: 26638882 DOI: 10.1002/ajmg.a.37494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 11/17/2015] [Indexed: 11/12/2022]
Abstract
This article reports a patient with a de novo ∼ 9.32 Mb duplication at 16p13.3 and a ∼ 71 Kb deletion at 22q13.33. The patient was followed from 1 month old to 3 years and 8 months of age and presented typical features of the 16p13.3 duplication syndrome. In addition, the patient presents a portal cavernoma, an alteration rarely reported in this condition. Renal agenesis was detected as additional developmental defect. After genomic array and FISH analysis, the karyotype was 46,XX,ins(22;16)(q13;p13.2p13.3). ish ins(22;16)(RP11-35P16+, RP11-27M24+). arr16p13.2p13.3(85,880-9,413,353)×3 dn arr22q13.33 (51,140,789-51,197,838)×1 dn. The authors provide a comprehensive review of the literature. This approach shed light on the genotype-phenotype correlation.
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Affiliation(s)
- Marshall I B Fontes
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil.,Medical Genetics Sector, State University of Health Sciences of Alagoas, Maceió, Alagoas, Brazil
| | - Ana P Santos
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Miriam C Molck
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Milena Simioni
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Diogo L L Nascimento
- Medical Genetics Sector, State University of Health Sciences of Alagoas, Maceió, Alagoas, Brazil
| | - Ana K M Andrade
- Clinical Genetics Service, Faculty of Medicine, University Hospital, Federal University of Alagoas-UFAL, Maceió, Alagoas, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana C V Krepischi
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Simone Appenzeller
- Department of Medical Clinical, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Isabella L Monlleó
- Clinical Genetics Service, Faculty of Medicine, University Hospital, Federal University of Alagoas-UFAL, Maceió, Alagoas, Brazil
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Edwards TJ, Sherr EH, Barkovich AJ, Richards LJ. Clinical, genetic and imaging findings identify new causes for corpus callosum development syndromes. ACTA ACUST UNITED AC 2014; 137:1579-613. [PMID: 24477430 DOI: 10.1093/brain/awt358] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The corpus callosum is the largest fibre tract in the brain, connecting the two cerebral hemispheres, and thereby facilitating the integration of motor and sensory information from the two sides of the body as well as influencing higher cognition associated with executive function, social interaction and language. Agenesis of the corpus callosum is a common brain malformation that can occur either in isolation or in association with congenital syndromes. Understanding the causes of this condition will help improve our knowledge of the critical brain developmental mechanisms required for wiring the brain and provide potential avenues for therapies for callosal agenesis or related neurodevelopmental disorders. Improved genetic studies combined with mouse models and neuroimaging have rapidly expanded the diverse collection of copy number variations and single gene mutations associated with callosal agenesis. At the same time, advances in our understanding of the developmental mechanisms involved in corpus callosum formation have provided insights into the possible causes of these disorders. This review provides the first comprehensive classification of the clinical and genetic features of syndromes associated with callosal agenesis, and provides a genetic and developmental framework for the interpretation of future research that will guide the next advances in the field.
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Affiliation(s)
- Timothy J Edwards
- 1 Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia2 Departments of Neurology and Pediatrics, The University of California and the Benioff Children's Hospital, CA, 94158, USA
| | - Elliott H Sherr
- 3 Departments of Pediatrics and Neurosurgery, Radiology and Biomedical Imaging, The University of California Children's Hospital, CA 94143, USA
| | - A James Barkovich
- 3 Departments of Pediatrics and Neurosurgery, Radiology and Biomedical Imaging, The University of California Children's Hospital, CA 94143, USA4 Departments of Paediatrics and Neurosurgery, Radiology and Biomedical Imaging, The University of California San Francisco and The Benioff Children's Hospital, CA 94143-0628 USA
| | - Linda J Richards
- 1 Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia5 School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
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16p subtelomeric duplication with vascular anomalies: an Albanian case report and literature review. Balkan J Med Genet 2013; 15:73-6. [PMID: 24052735 PMCID: PMC3776668 DOI: 10.2478/bjmg-2013-0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A patient with karyotype 46,XY,der(4) was recognized by standard cytogenetic techniques, and presented with facial features, neurological impairment and pulmonary hypertension. Multiplex ligation-dependent probe amplification (MLPA) demonstrated duplication of the subtelomeric region of chromosome 16p and deletion of the subtelomeric region of chromosome 4q, suggesting a translocation between 4q and 16p. The karyotype of his parents was normal and their MLPA analysis also indicated a de novo imbalance. He had microcephaly, high frontal hairline, thin blond hair, bilateral blepharophimosis and palpebral ptosis, short nose, everted upper lip, cleft palate, micrognathia, cupped anteverted ears, hypoplastic distal phalanges and bilateral inguinal hernia. He also had pulmonary hypertension with tricuspidal regurgitation; cavernous liver hemangioma anomalies have been previously described in association with dup16p. We concluded that pulmonary and other vascular anomalies can be a feature of dup16p. We believe this is the first confirmed case of a 16p subtelomeric duplication with vascular anomalies identified in Albania.
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El-Chammas KI, Venkatasubramani N, Veith R, Sekhri N, Rhead W, Toriello HV, Goday PS. Pancreatic insufficiency in Toriello-Carey syndrome: report of a second patient. Am J Med Genet A 2012; 158A:1208-11. [PMID: 22496049 DOI: 10.1002/ajmg.a.35304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 01/22/2012] [Indexed: 11/06/2022]
Abstract
Toriello-Carey syndrome is characterized by multiple congenital anomalies. Pancreatic insufficiency is suspected when patients present with poor weight gain, diarrhea, or maldigestion. The diagnosis is confirmed by low stool elastase and pancreatic stimulation testing. To our knowledge, only one patient with Toriello-Carey syndrome has been reported to have pancreatic insufficiency. We report on a second patient with Toriello-Carey syndrome and pancreatic insufficiency, and describe the management of pancreatic insufficiency in patients with this syndrome.
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Affiliation(s)
- Khalil I El-Chammas
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Chen CP, Ko TM, Su YN, Hsu CY, Chen YY, Su JW, Chen WL, Pan CW, Wang W. Prenatal diagnosis of partial trisomy 16p (16p12.2→pter) and partial monosomy 22q (22q13.31→qter) associated with increased nuchal translucency and abnormal maternal serum biochemistry in the first trimester. Taiwan J Obstet Gynecol 2012; 51:129-33. [DOI: 10.1016/j.tjog.2012.01.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2011] [Indexed: 11/26/2022] Open
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14
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Said E, Cuschieri A, Vermeesch J, Fryns JP. Toriello-Carey syndrome with a 6Mb interstitial deletion at 22q12 detected by array CGH. Am J Med Genet A 2011; 155A:1390-2. [DOI: 10.1002/ajmg.a.33961] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 01/26/2011] [Indexed: 11/10/2022]
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Hannachi H, Mougou-Zerelli S, BenAbdallah I, Mama N, Hamdi I, Labalme A, Elghezal H, Sanlaville D, Saad A. Clinical and Molecular Characterization of a Combined 17p13.3 Microdeletion with Partial Monosomy 21q21.3 in a 26-Year-Old Man. Cytogenet Genome Res 2011; 135:102-10. [DOI: 10.1159/000330880] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Chen CP, Su YN, Young RSH, Tsai FJ, Wu PC, Chern SR, Town DD, Pan CW, Wang W. Partial Trisomy 16p (16p12.2→pter) and Partial Monosomy 22q (22q13.31 →qter) Presenting With Fetal Ascites and Ventriculomegaly: Prenatal Diagnosis and Array Comparative Genomic Hybridization Characterization. Taiwan J Obstet Gynecol 2010; 49:506-12. [DOI: 10.1016/s1028-4559(10)60105-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2010] [Indexed: 10/18/2022] Open
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McGoey R, Varma A, Lacassie Y. Siblings with phenotypic overlap with Toriello-Carey syndrome and complex cytogenetic imbalances including 3q29 microduplication and 6p25 microdeletion: Review of the literature and additional evidence for genetic heterogeneity. Am J Med Genet A 2010; 152A:3068-73. [DOI: 10.1002/ajmg.a.33721] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Advanced age increases chromosome structural abnormalities in human spermatozoa. Eur J Hum Genet 2010; 19:145-51. [PMID: 21045871 DOI: 10.1038/ejhg.2010.166] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
This study explores the relationship between sperm structural aberrations and age by using a multicolor multichromosome FISH strategy that provides information on the incidence of duplications and deletions on all the autosomes. ToTelvysion kit (Abbott Molecular, Abbott Park, IL, USA) with telomere-specific probes was used. We investigated the sperm of 10 male donors aged from 23 to 74 years old. The donors were divided into two groups according to age, a cohort of five individuals younger than 40 and a cohort of five individuals older than 60 years. The goal of this study was to determine (1) the relationship between donor age and frequency and type of chromosome structural abnormalities and (2) chromosomes more frequently involved in sperm structural aberrations. We found that the older patients had a higher rate of structural abnormalities (6.6%) compared with the younger cohort (4.9%). Although both duplications and deletions were seen more frequently in older men, our findings demonstrate the presence of an excess of duplications versus deletions in both groups at a ratio of 2 to 1. We demonstrate that the distribution of duplications and deletions was not linear along the chromosomes, although a trend toward a higher rate of abnormalities in larger chromosomes was observed. This work is the first study addressing the frequencies of sperm chromosome structural aberrations of all autosomes in a single assay thus making a contribution to the clarification of the amount and origin of damage present in human spermatozoa and in relation to age.
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Distal trisomy 10q syndrome: phenotypic features in a child with inverted duplicated 10q25.1–q26.3. Clin Dysmorphol 2010; 19:140-145. [DOI: 10.1097/mcd.0b013e3283377915] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Digilio MC, Bernardini L, Capalbo A, Capolino R, Gagliardi MG, Marino B, Novelli A, Dallapiccola B. 16p subtelomeric duplication: a clinically recognizable syndrome. Eur J Hum Genet 2009; 17:1135-40. [PMID: 19293839 DOI: 10.1038/ejhg.2009.14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We report on two patients with duplication of the subterminal region of chromosome 16p (dup16p) recognized by fluorescent in situ hybridization (FISH) telomere analysis, presenting with closely overlapping facial features and neurological impairment. Distinct facial anomalies included high forehead, sparse eyebrows, blepharophimosis, short nose, everted upper lip, high-arched palate, wide-spaced teeth, and cupped anteverted ears. Susceptibility to vascular anomalies, in particular pulmonary hypertension and portal cavernoma, was found in one patient. Subtelomeric analysis by FISH demonstrated a de novo duplication of the subtelomeric region of chromosome 16p and a deletion of the subtelomeric region of chromosome 4q in case 1, and duplication of the subtelomeric region of 16p and a deletion of the subtelomeric region of 21q, resulting from malsegregation of a balanced maternal traslocation t(16pter;21qter) in case 2. The extension of duplicated regions measured by array-comparative genome hybridization was about 12 Mb on 16p13.3p13.13 in case 1, and about 8.5 Mb on 16p13.3p13.2 in case 2. In conclusion, we reported a clinically recognizable disorder in two patients with dup16p. Pulmonary hypertension, vascular ring, and manifestations of vascular disruption, as terminal hypoplasia of hands and aplasia cutis, have been previously described in association with dup16p. Thus, susceptibility to pulmonary vascular disease and other vascular anomalies can be a feature of dup16p, suggesting that this subtelomeric region in some respect could be related to vascular anomalies.
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Detailed characterization of, and clinical correlations in, 10 patients with distal deletions of chromosome 9p. Genet Med 2009; 10:599-611. [PMID: 18641517 DOI: 10.1097/gim.0b013e31817e2bde] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
PURPOSE Deletions of distal 9p are associated with trigonocephaly, mental retardation, dysmorphic facial features, cardiac anomalies, and abnormal genitalia. Previous studies identified a proposed critical region for the consensus phenotype in band 9p23, between 11.8 Mb and 16 Mb from the 9p telomere. Here we report 10 new patients with 9p deletions; 9 patients have clinical features consistent with 9p- syndrome, but possess terminal deletions smaller than most reported cases, whereas one individual lacks the 9p- phenotype and shows a 140-kb interstitial telomeric deletion inherited from his mother. METHODS We combined fluorescence in situ hybridization and microarray analyses to delineate the size of each deletion. RESULTS The deletion sizes vary from 800 kb to 12.4 Mb in our patients with clinically relevant phenotypes. Clinical evaluation and comparison showed little difference in physical features with regard to the deletion sizes. Severe speech and language impairment were observed in all patients with clinically relevant phenotypes. CONCLUSION The smallest deleted region common to our patients who demonstrate a phenotype consistent with 9p- is <2 Mb of 9pter, which contains six known genes. These genes may contribute to some of the cardinal features of 9p deletion syndrome.
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Marangi G, Leuzzi V, Orteschi D, Grimaldi ME, Lecce R, Neri G, Zollino M. Duplication of the Rubinstein-Taybi region on 16p13.3 is associated with a distinctive phenotype. Am J Med Genet A 2008; 146A:2313-7. [DOI: 10.1002/ajmg.a.32460] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray. Genet Med 2008; 10:415-29. [PMID: 18496225 DOI: 10.1097/gim.0b013e318177015c] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
PURPOSE Array comparative genomic hybridization is rapidly becoming an integral part of cytogenetic diagnostics. We report the design, validation, and clinical utility of an oligonucleotide array which combines genome-wide coverage with targeted enhancement at known clinically relevant regions. METHODS Probes were placed every 75 kb across the entire euchromatic genome to establish a chromosomal "backbone" with a resolution of approximately 500 kb, which is increased to approximately 50 kb in targeted regions. RESULTS For validation, 30 samples showed 100% concordance with previous G-banding and/or fluorescence in situ hybridization results. Prospective array analysis of 211 clinical samples identified 33 (15.6%) cases with clinically significant abnormalities. Of these, 23 (10.9%) were detected by the "targeted" coverage and 10 (4.7%) by the genome-wide coverage (average size of 3.7 Mb). All abnormalities were verified by fluorescence in situ hybridization, using commercially available or homebrew probes using the 32K bacterial artificial chromosome set. Four (1.9%) cases had previously reported imbalances of uncertain clinical significance. Five (2.4%) cases required parental studies for interpretation and all were benign familial variants. CONCLUSIONS Our results highlight the enhanced diagnostic utility of a genome-wide plus targeted array design, as the use of only a targeted array would have failed to detect 4.7% of the clinically relevant imbalances.
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Bonaglia MC, Giorda R, Beri S, Peters GB, Kirk EP, Hung D, Ciccone R, Gottardi G, Zuffardi O. Concurrent transposition of distal 6p and 20q to the 22q telomere: A recurrent benign chromosomal variant. Eur J Med Genet 2008; 51:148-55. [DOI: 10.1016/j.ejmg.2007.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Accepted: 11/23/2007] [Indexed: 12/08/2022]
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Mechanisms and consequences of small supernumerary marker chromosomes: from Barbara McClintock to modern genetic-counseling issues. Am J Hum Genet 2008; 82:398-410. [PMID: 18252220 DOI: 10.1016/j.ajhg.2007.10.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 10/05/2007] [Accepted: 10/18/2007] [Indexed: 11/22/2022] Open
Abstract
Supernumerary marker chromosomes (SMCs) are common, but their molecular content and mechanism of origin are often not precisely characterized. We analyzed all centromere regions to identify the junction between the unique chromosome arm and the pericentromeric repeats. A molecular-ruler clone panel for each chromosome arm was developed and used for the design of a custom oligonucleotide array. Of 27 nonsatellited SMCs analyzed by array comparative genomic hybridization (aCGH) and/or fluorescence in situ hybridization (FISH), seven (approximately 26%) were shown to be unique sequence negative. Of the 20 unique-sequence-positive SMCs, the average unique DNA content was approximately 6.5 Mb (range 0.3-22.2 Mb) and 33 known genes (range 0-149). Of the 14 informative nonacrocentric SMCs, five (approximately 36%) contained unique DNA from both the p and q arms, whereas nine (approximately 64%) contained unique DNA from only one arm. The latter cases are consistent with ring-chromosome formation by centromere misdivision, as first described by McClintock in maize. In one case, a r(4) containing approximately 4.4 Mb of unique DNA from 4p was also present in the proband's mother. However, FISH revealed a cryptic deletion in one chromosome 4 and reduced alpha satellite in the del(4) and r(4), indicating that the mother was a balanced ring and deletion carrier. Our data, and recent reports in the literature, suggest that this "McClintock mechanism" of small-ring formation might be the predominant mechanism of origin. Comprehensive analysis of SMCs by aCGH and FISH can distinguish unique-negative from unique-positive cases, determine the precise gene content, and provide information on mechanism of origin, inheritance, and recurrence risk.
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Niyazov DM, Nawaz Z, Justice AN, Toriello HV, Martin CL, Adam MP. Genotype/phenotype correlations in two patients with 12q subtelomere deletions. Am J Med Genet A 2008; 143A:2700-5. [PMID: 17937441 DOI: 10.1002/ajmg.a.32005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Subtelomeric imbalances have been implicated in developmental delay and mental retardation (MR) and described for most chromosomes. This study reports the first detailed description of two individuals with de novo 12q subtelomere deletions and high-resolution mapping of their deletion size with oligonucleotide array CGH for genotype/phenotype comparisons. Patient 1 is an 8-year-old male with borderline mild MR, food-seeking behavior, obesity, no significant dysmorphic facial features, abnormal hair whorl pattern, brachydactyly and mild clinodactyly. Patient 2 is a 12-year-old male with mild MR, food-seeking behavior, obesity, short stature, mild dysmorphic facial features, multicystic kidney and unilateral cryptorchidism. Both patients share a deleted region of approximately 1.6 Mb, including 14 known genes, which perhaps contributed to their similar phenotypes. However, Patient 2 has more severe MR and organ system involvement, possibly due to the larger deletion size ( approximately 4.5 Mb) including an additional eight genes, although it is difficult to make phenotype/genotype correlations based on only two patients. Due to the relatively mild presentation of both of our patients, we propose that a proportion of individuals with subtelomeric imbalances may go undetected and therefore, recommend subtelomeric studies be carried out for cases of unexplained mild MR or isolated learning disability (LD) with behavioral problems in the absence of major dysmorphic features or birth defects. In addition, 12q subtelomeric deletions should be considered in the differential diagnosis of patients presenting with food-seeking behavior and resultant obesity, as well as those referred to rule out Prader-Willi syndrome.
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Affiliation(s)
- Dmitriy M Niyazov
- Department of Human Genetics, Emory University School of Medicine, Decatur, GA 30033-5207, USA.
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Screening for subtelomeric chromosome alteration in a consecutive series of newborns with congenital defects. Clin Dysmorphol 2008; 17:5-12. [DOI: 10.1097/mcd.0b013e3282efef43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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28
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Roos A, Eggermann T, Zerres K, Schüler H. Polymorphic subtelomeric deletion 1q demonstrates the need to reevaluate subtelomere screening methods: Determination of the boundary between pathogenic deletion and benign variant for subtelomere 1q. Am J Med Genet A 2008; 146A:795-8. [DOI: 10.1002/ajmg.a.32222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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29
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Nowaczyk MJ, Carter MT, Xu J, Huggins M, Raca G, Das S, Martin CL, Schwartz S, Rosenfield R, Waggoner DJ. Paternal deletion 6q24.3: A new congenital anomaly syndrome associated with intrauterine growth failure, early developmental delay and characteristic facial appearance. Am J Med Genet A 2008; 146A:354-60. [DOI: 10.1002/ajmg.a.32144] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Vazna A, Havlovicova M, Sedlacek Z. Molecular cloning and analysis of breakpoints on ring chromosome 17 in a patient with autism. Gene 2008; 407:186-92. [DOI: 10.1016/j.gene.2007.10.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 10/02/2007] [Accepted: 10/05/2007] [Indexed: 10/22/2022]
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Thienpont B, Breckpot J, Holvoet M, Vermeesch JR, Devriendt K. A microduplication of CBP in a patient with mental retardation and a congenital heart defect. Am J Med Genet A 2007; 143A:2160-4. [PMID: 17702016 DOI: 10.1002/ajmg.a.31893] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Rubinstein-Taybi syndrome is a well-characterized genetic syndrome caused by haploinsufficiency of CBP in a majority of individuals. In 10% of cases a microdeletion in 16p13.3 affecting CBP is detected. We report on a patient with a de novo 345-480 kb micro-duplication the region, encompassing only CBP and TRAP1. This boy presented with various minor physical anomalies, moderate mental retardation, and an atrial septal defect, but none of the other typical characteristics of the Rubinstein-Taybi syndrome, such as the broad thumbs and first toes or facial characteristics. This finding implicates CBP as one of the causative genes for the trisomy 16p13 syndrome, and indicates this is a contiguous gene syndrome.
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Affiliation(s)
- Bernard Thienpont
- Center for Human Genetics, University Hospital Leuven, Leuven, Belgium
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Ballif BC, Sulpizio SG, Lloyd RM, Minier SL, Theisen A, Bejjani BA, Shaffer LG. The clinical utility of enhanced subtelomeric coverage in array CGH. Am J Med Genet A 2007; 143A:1850-7. [PMID: 17632771 DOI: 10.1002/ajmg.a.31842] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Telomeric chromosome abnormalities are a substantial cause of mental retardation and birth defects. Although subtelomeric fluorescence in situ hybridization (FISH) probes have been widely used to identify submicroscopic telomeric rearrangements, array-based comparative genomic hybridization (array CGH) has emerged as a more efficient and comprehensive detection method. Due to the clinical relevance of telomeric abnormalities, it has been proposed that array CGH using panels of BAC clones that map to regularly spaced intervals along the length of each telomere could be used to characterize subtelomeric aberrations more precisely in a single experiment. We have added 1,120 FISH-mapped BAC clones to our microarray to enhance the coverage of the 41 unique human subtelomeric regions. Contigs of clones were selected in increments of approximately 0.5 Mb beginning with the most distal unique sequence for each subtelomere and extending on average approximately 5.7 Mb toward the centromere. We have used this microarray to characterize 169 clinically significant subtelomeric abnormalities identified out of nearly 7,000 consecutive clinical cases analyzed by array CGH in our diagnostic laboratory. The expanded telomere coverage was sufficient to define the breakpoints of over half (56%) of the chromosome abnormalities. However, 44% of the subtelomeric aberrations extended beyond the size of this expanded coverage suggesting that many subtelomeric abnormalities are >5 Mb in size and that greater representation may be of even more value. In addition to identifying 6 cases of complex rearrangements, we have identified 42 cases of interstitial deletions that would have been missed by subtelomere FISH panels that use a single clone to the most distal unique sequence for each region. Microarrays designed to investigate regions known to be involved in chromosome abnormalities will enhance the detection of cytogenetic abnormalities at unprecedented resolution and frequency.
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Affiliation(s)
- Blake C Ballif
- Signature Genomic Laboratories, LLC, Spokane, Washington 99202, USA.
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Ruiter EM, Koolen DA, Kleefstra T, Nillesen WM, Pfundt R, de Leeuw N, Hamel BCJ, Brunner HG, Sistermans EA, de Vries BBA. Pure subtelomeric microduplications as a cause of mental retardation. Clin Genet 2007; 72:362-8. [PMID: 17850634 DOI: 10.1111/j.1399-0004.2007.00874.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Submicroscopic subtelomeric aberrations are a common cause of mental retardation (MR). New molecular techniques allow the identification of subtelomeric microduplications, but their frequency and significance are largely unknown. We determined the frequency of subtelomeric, pure microduplications in a cohort of 624 patients with MR and/or multiple congenital anomalies using multiplex ligation dependent probe amplification (MLPA) and delineated the identified microduplications using array based comparative genomic hybridization (array CGH). In 11 patients, MLPA revealed a subtelomeric duplication without a concurrent deletion. Additional fluorescence in situ hybridization studies and parental analyses showed that three had occurred de novo: one duplication 5q34qter (12.7 Mb), one duplication 9q34.13qter (7.2 Mb) and one duplication 9p24.2pter (4.1 Mb). Five microduplications (9p, 11q, 12q, 15q and 16p) appeared to be inherited from an unaffected parent, while in three cases (9p, 12p and 17p) the parents were not available for testing. Based on our findings and data from the literature, the three de novo duplications were the only ones likely to be disease-causing, leading to a frequency of pathogenic subtelomeric, pure microduplications of 0.5%. Our study shows that subtelomeric microduplications are an infrequent cause of MR and that additional clinical and family studies are required to assess their clinical significance.
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Affiliation(s)
- E M Ruiter
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands
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Martin CL, Duvall JA, Ilkin Y, Simon JS, Arreaza MG, Wilkes K, Alvarez-Retuerto A, Whichello A, Powell CM, Rao K, Cook E, Geschwind DH. Cytogenetic and molecular characterization of A2BP1/FOX1 as a candidate gene for autism. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:869-76. [PMID: 17503474 DOI: 10.1002/ajmg.b.30530] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cytogenetic imbalances are increasingly being realized as causes of autism. Here, we report a de novo translocation between the short arms of chromosomes 15 and 16 in a female with autism, epilepsy, and global developmental delay. FISH analysis identified a cryptic deletion of approximately 160 kb at the boundary of the first exon and first intron of the 1.7 Mb ataxin-2 binding protein-1 (A2BP1) gene, also called FOX1. Quantitative real time PCR (Q-PCR) analysis verified a deletion of exon 1 in the 5' promoter region of the A2BP1 gene. Reverse transcription PCR (qRT-PCR) showed reduced mRNA expression in the individual's lymphocytes, demonstrating the functional consequence of the deletion. A2BP1 codes for a brain-expressed RNA binding or splicing factor. Because of emerging evidence in the role of RNA processing and gene regulation in pervasive developmental disorders, we performed further screening of A2BP1 in additional individuals with autism from the Autism Genetics Resource Exchange (AGRE) collection. Twenty-seven SNPs were genotyped across A2BP1 in 206 parent-child trios and two regions showed association at P < or = 0.008 level. No additional deletions or clear mutations were identified in 88 probands by re-sequencing of all exons and surrounding intronic regions or quantitative PCR (Q-PCR) of exon 1. Although only nominal association was observed, and no obvious causal mutations were identified, these results suggest that A2BP1 may affect susceptibility or cause autism in a subset of patients. Further investigations in a larger sample may provide additional information regarding the involvement of this gene in the autistic phenotype.
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Martin CL, Nawaz Z, Baldwin EL, Wallace EJ, Justice AN, Ledbetter DH. The evolution of molecular ruler analysis for characterizing telomere imbalances: from fluorescence in situ hybridization to array comparative genomic hybridization. Genet Med 2007; 9:566-73. [PMID: 17873644 DOI: 10.1097/gim.0b013e318149e1fc] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Submicroscopic telomere imbalances are a significant cause of mental retardation with or without other phenotypic abnormalities. We previously developed a set of unique telomere clones that identify imbalances in 3% to 5% of children with unexplained mental retardation and a normal karyotype. This targeted screening approach, however, does not provide information about the size or gene content of the imbalance. To enable such comprehensive characterization, a "molecular ruler" clone panel, extending up to 5 Mb proximal to the first telomere clone for each chromosome arm, was developed. This panel of clones was successfully used to delineate the size of unbalanced telomere aberrations in a fluorescence in situ hybridization assay. However, the fluorescence in situ hybridization analysis was quite labor-intensive, and for many cases, the imbalance extended beyond our 5-Mb coverage. Therefore, to develop a more efficient and comprehensive method for characterizing telomere imbalances, we developed a custom oligonucleotide microarray consisting of high-density coverage of all telomere regions as well as a whole-genome backbone. Overall, 44 pathogenic imbalances studied by fluorescence in situ hybridization or oligonucleotide array showed a size range of 400 kb to 13.5 Mb. In four of these, the array detected additional interstitial imbalances adjacent to the telomere imbalance, demonstrating the usefulness of added probe coverage. In 10 cases with benign imbalances inherited from a normal parent, the size ranged from 170 kb to 1.6 Mb. These results demonstrate that array comparative genomic hybridization will aid in more efficient and precise characterization of telomere imbalances leading to the development of gene dosage maps at human telomere regions for genotype/phenotype correlations.
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Affiliation(s)
- Christa Lese Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
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Lee C, Iafrate AJ, Brothman AR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet 2007; 39:S48-54. [PMID: 17597782 DOI: 10.1038/ng2092] [Citation(s) in RCA: 264] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The recent appreciation of widespread copy number variation in the genomes of healthy human beings has presented a significant challenge to clinical cytogeneticists who wish to use genome-wide array comparative genomic hybridization (CGH) assays for clinical diagnostic purposes. Clinical cytogeneticists need to differentiate between copy number variants (CNVs) that are likely to be pathogenic and CNVs that are less likely to contribute to an affected individual's clinical presentation. Unfortunately, our knowledge of the phenotypic effects of most CNVs is minimal, leading to the classification of many CNVs as genomic imbalances of unknown clinical significance. This has caused many laboratories to resist the use of higher-resolution genome-wide array CGH assays for clinical purposes. Ironically, the accumulation and annotation of such array CGH data can lead to the rapid identification of pathogenic CNVs and the definition of new genomic syndromes that, in turn, are useful for accurate clinical genetic diagnoses.
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Affiliation(s)
- Charles Lee
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.
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Orellana C, Monfort S, Roselló M, Oltra S, Martínez F. Clinical findings and molecular characterization of six subtelomeric imbalances. Clin Genet 2007; 71:474-9. [PMID: 17489855 DOI: 10.1111/j.1399-0004.2007.00792.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Bejjani BA, Theisen AP, Ballif BC, Shaffer LG. Array-based comparative genomic hybridization in clinical diagnosis. Expert Rev Mol Diagn 2007; 5:421-9. [PMID: 15934818 DOI: 10.1586/14737159.5.3.421] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The sequencing of the human genome and development of high-throughput microarray technologies have enhanced the detection of copy number alterations in cancer research and the study of constitutional chromosomal abnormalities. Microarray-based comparative genomic hybridization (array CGH) has integrated molecular and traditional cytogenetics and has begun to impact the clinician's approach to medical genetics. Clinical applications of array CGH may define new genetic syndromes, expand the phenotype of existing syndromes and characterize a genomic signature of some cancers. As array CGH becomes the initial diagnostic approach for the investigation of constitutional and acquired chromosomal abnormalities, the combination of bioinformatics, robotics and microarray technology will set the stage for a new generation of high-resolution and high-throughput tools for genetic analysis, diagnosis and gene discovery.
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Affiliation(s)
- Bassem A Bejjani
- Signature Genomic Laboratories, 44 West 6th Avenue, Suite 202, Spokane, WA 99204, USA.
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Balikova I, Menten B, de Ravel T, Le Caignec C, Thienpont B, Urbina M, Doco-Fenzy M, de Rademaeker M, Mortier G, Kooy F, van den Ende J, Devriendt K, Fryns JP, Speleman F, Vermeesch JR. Subtelomeric imbalances in phenotypically normal individuals. Hum Mutat 2007; 28:958-67. [PMID: 17492636 DOI: 10.1002/humu.20537] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Subtelomeric imbalances are identified in approximately 5% of patients with idiopathic mental retardation (MR) and multiple congenital anomalies (MCA). Because of this high incidence, screening for subtelomeric anomalies became part of the routine genetic evaluation of MCA/MR patients. In contrast to the general view that subtelomeric imbalances cause MCA/MR, we report here 15 subtelomeric copy-number changes in 12 families in which the imbalance is inherited from a phenotypically normal parent. We detected inherited deletions at subtelomeres 2q, 3p, 4p, 4q, 6q, 10q, 17p, 17q, Xp, and Yq and duplications at 1q, 4q, 10q, and 11q. Interestingly, in addition to small deletions (<1 Mb) also unexpected large deletions and duplications up to 7.8 Mb were detected. Taken together with previous reports, a total of 16 subtelomeric duplications and 18 deletions inherited from a phenotypically normal parent have now been reported. Clearly, more extensive genotype-phenotype correlations are needed to better understand the phenotypic consequences of these subtelomeric copy number variations and to resolve the current uncertainty for genetic counseling in postnatal and prenatal diagnosis.
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Affiliation(s)
- Irina Balikova
- Center for Human Genetics, University Hospital Gasthuisberg, Leuven, Belgium
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Zou YS, Van Dyke DL, Ellison JW. Microarray comparative genomic hybridization and FISH studies of an unbalanced cryptic telomeric 2p deletion/16q duplication in a patient with mental retardation and behavioral problems. Am J Med Genet A 2007; 143A:746-51. [PMID: 17345620 DOI: 10.1002/ajmg.a.31645] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a 7-year-old patient with pervasive developmental disorder and behavioral problems who has a de novo cryptic unbalanced der(2)t(2;16)(p25.3;q24.3) chromosome resulting in deletion of distal 2p and duplication of distal 16q. These segmental aneusomies were detected by microarray comparative genomic hybridization analysis, as was a distal 17p13.3 duplication that was inherited from her father. FISH analysis using bacterial artificial chromosomes confirmed a deletion of approximately 1,700 kbp of DNA from 2pter (containing at least six complete genes or transcription units) and a duplication of approximately 500 kbp from 16qter (including up to ten genes or transcription units). Several genes in these regions are plausible candidates for contributing to the patient's phenotype.
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Affiliation(s)
- Ying S Zou
- Cytogenetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
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Morales C, Soler A, Margarit E, Madrigal I, Sánchez A. Trisomy of 19.4 Mb region of chromosome 22 and subtelomeric 17p identified in a male without clinical affectation. Am J Med Genet A 2007; 143A:2423-9. [PMID: 17853459 DOI: 10.1002/ajmg.a.31777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Supernumerary marker chromosomes (SMCs) have a reported frequency in the prenatal and newborn population ranging from 0.04% to 0.08% and about 37% of diagnosed SMCs are associated with an abnormal phenotype. Around 7.5% of them are derived from chromosome 22. SMCs(22) that result in tri- or tetrasomy of band 22q11.2 are associated with Cat-eye syndrome (CES), a syndrome of variable penetrance and affectation. CES-like phenotype has been also related to 22q11.2 interstitial duplications and der(22) syndrome. The 22q11.2 region, also involved in the velocardiofacial microdeletional syndrome, presents high susceptibility to chromosomal rearrangements due to the presence of low-copy repeats sequences (LCR22). Another region in the genome rich in LCR is 17p and five recurrent disorders have been mapped on the region 17p11-p13. Some chromosomal imbalances affecting the 17p13.3 subtelomeric region have been reported, related to cryptic unbalanced translocations and associated, in most cases, to mental retardation and dysmorphic features. We report on a healthy male carrier of a SMC that was identified as a +der(22)t(17;22)(p13.3;q11.2) consequence of an abnormal 3:1 segregation of the paternal t(17;22) and we have determined the approximate size of the trisomic regions, comparing the obtained results with other reported imbalances involving 22q11.2 and 17pter.
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Affiliation(s)
- Carme Morales
- Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain
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Ledbetter DH, Martin CL. Cryptic telomere imbalance: A 15-year update. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2007; 145C:327-34. [PMID: 17910073 DOI: 10.1002/ajmg.c.30149] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
It has been 15 years since we proposed that assays of telomere integrity might reveal cryptic translocations and deletions as a significant cause of mental retardation (MR) in patients with normal G-banded karyotypes. Development of unique genomic probes adjacent to the subtelomeric repeats of each chromosome arm allowed multiplex FISH analyses that confirmed such cryptic telomeric imbalances in 3-6% of all unexplained MR. Although such "telomere FISH" analysis quickly became standard of care, limitations of this technology platform included a lack of information on the size and gene content of the deleted/duplicated segments and the failure to detect interstitial deletions not involving the most distal unique clone. The development of "molecular ruler" clone sets for every human telomere provided the foundation for accurate determination of size and gene content of each imbalance, as well as the detection of interstitial deletions within these regions. Array comparative genomic hybridization (aCGH) has emerged as a powerful technology to assess single copy changes (monosomy or trisomy) at targeted loci such as telomeres or across the whole genome. This technology now replaces multiplex FISH for the assessment of telomere integrity in unexplained MR and has the advantage of efficiently determining the size and gene content of the imbalance, as well as detecting interstitial deletions near telomeres or anywhere else in the genome covered by the array design. The application of aCGH in several studies of unexplained MR has confirmed that telomere imbalances are overrepresented compared to "average" chromosomal regions, although this is likely due to random chromosome breakage rather than specific molecular mechanisms associated with the genomic architecture of human telomeres. Telomere imbalances are significantly larger than initially envisioned ( approximately 40% are >5 Mb in size), and indicate the analytic sensitivity of the G-banded karyotype is much lower than previously thought. Finally, experience with smaller benign variants compared to larger pathogenic imbalances at telomeres serves as a model for approaching whole-genome aCGH in a clinical setting.
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Affiliation(s)
- David H Ledbetter
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA 30322, USA.
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Toriello HV, Hatchwell E. Toriello-Carey syndrome phenotype and chromosome anomalies. Am J Med Genet A 2007; 146A:116. [DOI: 10.1002/ajmg.a.32057] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Knight SJL, Regan R. Idiopathic learning disability and genome imbalance. Cytogenet Genome Res 2006; 115:215-24. [PMID: 17124403 DOI: 10.1159/000095917] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Accepted: 04/28/2006] [Indexed: 12/08/2022] Open
Abstract
Learning disability (LD) is a very common, lifelong and disabling condition, affecting about 3% of the population. Despite this, it is only over the past 10-15 years that major progress has been made towards understanding the origins of LD. In particular, genetics driven advances in technology have led to the unequivocal demonstration of the importance of genome imbalance in the aetiology of idiopathic LD (ILD). In this review we provide an overview of these advances, discussing technologies such as multi-telomere FISH and array CGH that have already emerged as well as new approaches that show diagnostic potential for the future. The advances to date have highlighted new considerations such as copy number polymorphisms (CNPs) that can complicate the interpretation of genome imbalance and its relevance to ILD. More importantly though, they have provided a remarkable approximately 15-20% improvement in diagnostic capability as well as facilitating genotype/phenotype correlations and providing new avenues for the identification and understanding of genes involved in neurocognitive function.
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Affiliation(s)
- S J L Knight
- Oxford Genetics Knowledge Park, Wellcome Trust Centre for Human Genetics, University of Oxford, UK.
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Bonaglia MC, Marelli S, Gottardi G, Zucca C, Pramparo T, Giorda R, Grasso R, Borgatti R, Zuffardi O. Subtelomeric trisomy 21q: a new benign chromosomal variant. Eur J Med Genet 2006; 50:54-9. [PMID: 17055792 DOI: 10.1016/j.ejmg.2006.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Accepted: 07/28/2006] [Indexed: 11/21/2022]
Abstract
The diagnosis of a subtelomeric rearrangement has immediate impact on counseling, particularly in the case of familial rearrangements. However, the existence of subtelomeric imbalances with absent phenotypic effects may hamper genetic counseling, particularly when the rearrangement has not been previously described. We report on a new subtelomeric polymorphism, consisting of a familial subtelomeric rearrangement of chromosome 19 resulting in distal trisomy for 21q, detected in a child with Angelman Syndrome (AS) due to an UBE3A mutation. This report shows that new, previously unknown, benign subtelomeric variants may complicate the correct clinical diagnosis.
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Shaffer LG, Kashork CD, Saleki R, Rorem E, Sundin K, Ballif BC, Bejjani BA. Targeted genomic microarray analysis for identification of chromosome abnormalities in 1500 consecutive clinical cases. J Pediatr 2006; 149:98-102. [PMID: 16860135 DOI: 10.1016/j.jpeds.2006.02.006] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 01/26/2006] [Accepted: 02/07/2006] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To assess the yield of array-based comparative genomic hybridization. STUDY DESIGN The results of array comparative genomic hybridization were collected on 1500 consecutive clinical cases sent to our laboratory for a variety of developmental problems. Confirmation fluorescence in situ hybridization of metaphase or interphase cells, depending on the aberration, was performed. RESULTS Of the 1500 cases, 134 (8.9%) showed an abnormality: 36 (2.4%) showed polymorphisms or familial variants, 14 (0.9%) showed alterations of unknown clinical significance, and 84 (5.6%) showed clinically relevant genomic alterations. These included subtelomeric deletions and unbalanced rearrangements, microdeletions and reciprocal duplications, rare abnormalities, and low-level trisomy mosaicism. CONCLUSIONS A targeted array detects a substantial proportion of abnormalities even in those patients who have already had extensive cytogenetic and/or fluorescence in situ hybridization testing. This study, although not a controlled ascertainment of subjects with specific selection criteria, accurately reflects the reality of clinical cytogenetic practice and provides an estimate of the cytogenetic abnormalities that can be identified with a targeted microarray in a diagnostic laboratory. Microarray analysis likely doubles the current yield of abnormal results detected by conventional cytogenetic analysis.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, LLC, Spokane, Washington, USA.
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Abstract
In total, 200 families were reviewed with directly transmitted, cytogenetically visible unbalanced chromosome abnormalities (UBCAs) or euchromatic variants (EVs). Both the 130 UBCA and 70 EV families were divided into three groups depending on the presence or absence of an abnormal phenotype in parents and offspring. No detectable phenotypic effect was evident in 23/130 (18%) UBCA families ascertained mostly through prenatal diagnosis (group 1). In 30/130 (23%) families, the affected proband had the same UBCA as other phenotypically normal family members (group 2). In the remaining 77/130 (59%) families, UBCAs had consistently mild consequences (group 3). In the 70 families with established EVs of 8p23.1, 9p12, 9q12, 15q11.2, and 16p11.2, no phenotypic effect was apparent in 38/70 (54%). The same EV was found in affected probands and phenotypically normal family members in 30/70 families (43%) (group 2), and an EV co-segregated with mild phenotypic anomalies in only 2/70 (3%) families (group 3). Recent evidence indicates that EVs involve copy number variation of common paralogous gene and pseudogene sequences that are polymorphic in the normal population and only become visible at the cytogenetic level when copy number is high. The average size of the deletions and duplications in all three groups of UBCAs was close to 10 Mb, and these UBCAs and EVs form the "Chromosome Anomaly Collection" at http://www.ngrl.org.uk/Wessex/collection. The continuum of severity associated with UBCAs and the variability of the genome at the sub-cytogenetic level make further close collaboration between medical and laboratory staff essential to distinguish clinically silent variation from pathogenic rearrangement.
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Affiliation(s)
- J C K Barber
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire SP2 8BJ, UK.
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Lam ACF, Lam STS, Lai KKS, Tong TMF, Chau TC. High rate of detection of subtelomeric aberration by using combined MLPA and subtelomeric FISH approach in patients with moderate to severe mental retardation. Clin Biochem 2006; 39:196-202. [PMID: 16497288 DOI: 10.1016/j.clinbiochem.2006.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 11/17/2005] [Accepted: 01/02/2006] [Indexed: 12/21/2022]
Abstract
OBJECTIVES (1) To evaluate the prevalence of subtelomeric deletion in moderate to severe mental retardation population, (2) to assess the feasibility and cost-effectiveness of combined methodology in routine workup of this sub-population. METHOD Twenty unrelated patients using strict selection criteria were recruited for the study from the Clinical Genetic Service. Patients were initially screened by Multiplex Ligation-dependent Probe Amplification (MLPA) for subtelomeric imbalance followed by FISH analysis for anatomical integrity. This is then followed by parental subtelomeric FISH analysis. RESULTS Three subtelomeric deletions were identified. They were Deletion 1p36, Deletion 1q44 and Deletion 10q26; these were previously unidentified by conventional technique. CONCLUSIONS The prevalence of subtelomeric deletion in our cohort of moderate to severe mental retardation patients is consistent with published findings of around 10%. The figure is on the higher side if more stringent criteria is used. The combination of strict clinical criteria, MLPA and selective subtelomeric FISH was shown to be feasible and cost-effective.
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Affiliation(s)
- Albert C F Lam
- Clinical Genetic Service, Department of Health, HKSAR Government, Cheung Sha Wan, Kowloon, Hong Kong.
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Moog U, Arens YHJM, van Lent-Albrechts JCM, Huijts PEA, Smeets EEJ, Schrander-Stumpel CTRM, Engelen JJM. Subtelomeric chromosome aberrations: still a lot to learn. Clin Genet 2005; 68:397-407. [PMID: 16207207 DOI: 10.1111/j.1399-0004.2005.00506.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Subtelomeric chromosome aberrations: still a lot to learn.Cryptic subtelomeric chromosome aberrations are a significant cause of mental retardation (MR). More than 4000 patients have been investigated, and the mean overall prevalence of subtelomeric rearrangements has been found to be 5.2%. In order to contribute to knowledge on the clinical presentation of subtelomeric rearrangements, we retrospectively studied patients with unexplained MR who had been evaluated for subtelomeric abnormalities by different fluorescence in situ hybridization (FISH) techniques. Hundred and two patients had an unexplained combination of MR with dysmorphism, congenital anomalies, and/or a positive family history and were investigated by total subtelomeric (TS) FISH (89/102), or by total painting (TP) in an obligate carrier in the case of familial MR (13/102). In 59 additional patients, a sequence-specific FISH was performed on clinical indication. In the 102 patients studied by TS or TP, six pathogenic aberrations (5.9%) were found in addition to one polymorphism. In total, eight clinically significant subtelomeric aberrations were found in the 161 index patients; four of these eight aberrations were familial. We report on the clinical presentation of all patients with an aberration and review the relevant literature. Factors complicating the interpretation of subtelomeric rearrangements are discussed, such as the occurrence of variants, clinical variability, and limited knowledge of the phenotype.
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Affiliation(s)
- U Moog
- Department of Clinical Genetics, University Hospital Maastricht, the Netherlands.
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Abstract
Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.
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Affiliation(s)
- Daniel Pinkel
- Comprehensive Cancer Center, Department of Laboratory Medicine, University of California, San Francisco, California 94143, USA.
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