1
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Niceta M, Pizzi S, Inzana F, Peron A, Bakhtiari S, Nizon M, Levy J, Mancini C, Cogné B, Radio FC, Agolini E, Cocciadiferro D, Novelli A, Salih MA, Recalcati MP, Arancio R, Besnard M, Tabet A, Kruer MC, Priolo M, Dallapiccola B, Tartaglia M. Delineation of the clinical profile of CNOT2 haploinsufficiency and overview of the IDNADFS phenotype. Clin Genet 2023; 103:156-166. [PMID: 36224108 PMCID: PMC9939052 DOI: 10.1111/cge.14247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 01/07/2023]
Abstract
CNOT2 haploinsufficiency underlies a rare neurodevelopmental disorder named Intellectual Developmental disorder with NAsal speech, Dysmorphic Facies, and variable Skeletal anomalies (IDNADFS, OMIM 618608). The condition clinically overlaps with chromosome 12q15 deletion syndrome, suggesting a major contribution of CNOT2 haploinsufficiency to the latter. CNOT2 is a member of the CCR4-NOT complex, which is a master regulator of multiple cellular processes, including gene expression, RNA deadenylation, and protein ubiquitination. To date, less than 20 pathogenic 12q15 microdeletions encompassing CNOT2, together with a single truncating variant of the gene, and two large intragenic deletions have been reported. Due to the small number of affected subjects described so far, the clinical profile of IDNADFS has not been fully delineated. Here we report five unrelated individuals, three of which carrying de novo intragenic CNOT2 variants, one presenting with a multiexon intragenic deletion, and an additional case of 12q15 microdeletion syndrome. Finally, we assess the features of IDNADFS by reviewing published and present affected individuals and reevaluate the clinical phenotype of this neurodevelopmental disorder.
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Affiliation(s)
- Marcello Niceta
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
- Department of PediatricsSapienza UniversityRomeItaly
| | - Simone Pizzi
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Francesca Inzana
- Genetic Counseling ServiceRegional Hospital of BolzanoBolzanoItaly
| | - Angela Peron
- Medical GeneticsASST Santi Paolo e Carlo, Ospedale San PaoloMilanItaly
- Division of Medical Genetics, Department of PediatricsUniversity of UtahSalt Lake CityUtahUSA
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric NeurologyBarrow Neurological Institute, Phoenix Children's HospitalPhoenixArizonaUSA
- Departments of Child Health, Neurology, and Cellular and Molecular Medicine, and Program in GeneticsUniversity of Arizona College of Medicine – PhoenixPhoenixArizonaUSA
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique MédicaleL'institut du thorax, INSERM, CNRS, UNIV NantesNantesFrance
| | - Jonathan Levy
- Genetics DepartmentAP‐HP, Robert‐Debré University HospitalParisFrance
| | - Cecilia Mancini
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Benjamin Cogné
- Laboratoire de Génétique MoléculaireCHU de NantesNantesFrance
| | | | - Emanuele Agolini
- Translational Cytogenomics Research UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Dario Cocciadiferro
- Translational Cytogenomics Research UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Antonio Novelli
- Translational Cytogenomics Research UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Mustafa A. Salih
- Neurology Division, Department of PediatricsCollege of Medicine, King Saud UniversityRiyadhSaudi Arabia
- Department of PediatricsCollege of Medicine, Almughtaribeen UniversityKhartoumSudan
| | - Maria Paola Recalcati
- Medical Cytogenetics LaboratoryIstituto Auxologico Italiano IRCCSCusano MilaninoItaly
| | - Rosangela Arancio
- Clinica PediatricaOspedale San Paolo, ASST Santi Paolo CarloMilanItaly
| | - Marianne Besnard
- Service de NéonatologieCentre Hospitalier de Polynésie FrançaisePapeeteFrench Polynesia
| | - Anne‐Claude Tabet
- Human Genetics and Cognitive FunctionsInstitut Pasteur, UMR3571 CNRS, Université de ParisParisFrance
- Cytogenetic UnitRobert Debré Hospital, APHPParisFrance
| | - Michael C. Kruer
- Departments of Child Health, Neurology, and Cellular and Molecular Medicine, and Program in GeneticsUniversity of Arizona College of Medicine – PhoenixPhoenixArizonaUSA
| | - Manuela Priolo
- UOSD Genetica MedicaGrande Ospedale Metropolitano “Bianchi‐Melacrino‐Morelli”Reggio CalabriaItaly
| | - Bruno Dallapiccola
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Marco Tartaglia
- Genetics and Rare DiseasesBambino Gesù Children's Hospital, IRCCSRomeItaly
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2
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Di Nora A, De Costa G, Di Mari A, Montemagno M, Pavone V, Pavone P. A New 12q21 Deletion Syndrome: A Case Report and Literature Review. Glob Med Genet 2022; 9:214-218. [PMID: 35873668 PMCID: PMC9303074 DOI: 10.1055/s-0042-1748171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Diagnosis in children with physical and intellective anomalies is very challenging because of the wide spectrum of causes. Array-based comparative genomic hybridization (CGH) has acquired an important role in pediatric diagnostic work up. Interstitial deletion of the long arm of chromosome 12 are rare. To date, deletions including the 12q21 region were reported in only 13 patients. The main features are development delay, eyes and central nervous system anomalies, and heart and kidney defects. We describe a 3-year-old boy with a de novo 15 Mb deletion at 12q21.1q21.32, never reported in the last cases. By screening the critical region and reviewing the literature, we identified SYT1, PPP1R12A, and CEP290 such as pathogenetic genes.
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Affiliation(s)
- Alessandra Di Nora
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Greta De Costa
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alessia Di Mari
- Department of Radiology, University of Catania, Catania, Italy
| | - Marco Montemagno
- Department of General Surgery and Medical Surgical Specialties, Section of Orthopaedics and Traumatology, University Hospital Policlinico-San Marco, University of Catania, Catania, Italy
| | - Vito Pavone
- Department of General Surgery and Medical Surgical Specialties, Section of Orthopaedics and Traumatology, University Hospital Policlinico-San Marco, University of Catania, Catania, Italy
| | - Piero Pavone
- Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, Hospital “Policlinico G. Rodolico,” Catania, Italy
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3
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12q21 Interstitial Deletions: Seven New Syndromic Cases Detected by Array-CGH and Review of the Literature. Genes (Basel) 2022; 13:genes13050780. [PMID: 35627165 PMCID: PMC9141874 DOI: 10.3390/genes13050780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 02/04/2023] Open
Abstract
Interstitial deletions of the long arm of chromosome 12 are rare, with a dozen patients carrying a deletion in 12q21 being reported. Recently a critical region (CR) has been delimited and could be responsible for the more commonly described clinical features, such as developmental delay/intellectual disability, congenital genitourinary and brain malformations. Other, less frequent, clinical signs do not seem to be correlated to the proposed CR. We present seven new patients harboring non-recurrent deletions ranging from 1 to 18.5 Mb differentially scattered across 12q21. Alongside more common clinical signs, some patients have rarer features such as heart defects, hearing loss, hypotonia and dysmorphisms. The correlation of haploinsufficiency of genes outside the CR to specific signs contributes to our knowledge of the effect of the deletion of this gene-poor region of chromosome 12q. This work underlines the still important role of copy number variations in the diagnostic setting of syndromic patients and the positive reflection on management and family genetic counseling.
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4
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Royer-Bertrand B, Cisarova K, Niel Bütschi F, Foletti G, Guinchat V, Tran C, Superti-Furga A, Good JM. CNOT2 haploinsufficiency in a 40-year-old man with intellectual disability, autism, and seizures. Am J Med Genet A 2021; 185:2602-2606. [PMID: 34018673 DOI: 10.1002/ajmg.a.62343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/08/2021] [Accepted: 04/30/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Beryl Royer-Bertrand
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Katarina Cisarova
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Florence Niel Bütschi
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Giovanni Foletti
- Neurology-Epileptology, Institution of Lavigny, Lavigny, Switzerland
| | - Vincent Guinchat
- Department of Psychiatry, Psychiatric Section of Mental Development, Lausanne University Hospital (CHUV), Prilly-Lausanne, Switzerland
| | - Christel Tran
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
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5
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Niclass T, Le Guyader G, Beneteau C, Joubert M, Pizzuti A, Giuffrida MG, Bernardini L, Gilbert-Dussardier B, Bilan F, Egloff M. 12q21 deletion syndrome: Narrowing the critical region down to 1.6 Mb including SYT1 and PPP1R12A. Am J Med Genet A 2020; 182:2133-2138. [PMID: 32633079 DOI: 10.1002/ajmg.a.61734] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/04/2020] [Accepted: 05/21/2020] [Indexed: 11/12/2022]
Abstract
Deletions in the 12q21 region are rare and non-recurrent CNVs. To date, only 11 patients with deletions in this region have been reported in the literature. These patients most often presented with syndromic intellectual deficiency, ventriculomegaly or hydrocephalus, ectodermal abnormalities, growth retardation and renal and cardiac malformations, suggesting a recognizable microdeletion syndrome. We report three new patients with overlapping deletions of the 12q21 region, including the smallest deletion reported to date and the first case characterized by array CGH during pregnancy. We describe specific clinical findings and shared facial features as developmental delay, ectodermal abnormalities, ventriculomegaly or hydrocephalus, axial hypotonia or spastic diplegia, growth retardation, heart defect, hydronephrosis, ureteral reflux or horseshoe kidney, large thorax or pectus excavatum, syndactyly of 2-3 toes, pterygium coli or excess nuchal skin, large anterior fontanel, low set ears, prominent forehead, short-upturned nose with nostril hypoplasia, microretrognathia and hypertelorism. These new patients and a comprehensive review of the literature allow us to define a minimum critical region spanning 1.6 Mb in 12q21. By screening the critical region using prediction tools, we identified two candidate genes: SYT1and PPP1R12A.
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Affiliation(s)
- Tanguy Niclass
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
| | - Gwenael Le Guyader
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,EA 3808 NEUVACOD, Université de Poitiers, Poitiers, France
| | - Claire Beneteau
- Department of Medical Genetics, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Madeleine Joubert
- Department of Anatomic and Fetal Pathology, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Antonio Pizzuti
- Department of Medical Genetics, Policlinico di Roma, Rome, Italy
| | - Maria Grazia Giuffrida
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cytogenetics Unit, San Giovanni Rotondo, FG, Italy
| | - Laura Bernardini
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cytogenetics Unit, San Giovanni Rotondo, FG, Italy
| | - Brigitte Gilbert-Dussardier
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,EA 3808 NEUVACOD, Université de Poitiers, Poitiers, France
| | - Frederic Bilan
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,EA 3808 NEUVACOD, Université de Poitiers, Poitiers, France
| | - Matthieu Egloff
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Experimentales et Cliniques, INSERM, Poitiers, France
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6
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Baldan F, Passon N, Burra S, Demori E, Russo PD, Damante G. Quantitative PCR evaluation of deletions/duplications identified by array CGH. Mol Cell Probes 2019; 46:101421. [PMID: 31302230 DOI: 10.1016/j.mcp.2019.101421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 12/01/2022]
Abstract
Genomic deletions/duplications detected by array comparative genomic hybridization (aCGH) should be confirmed by an independent technology. This approach allows also to test, at low cost, inheritance of the imbalance. In the present study we explored the use of quantitative PCR (qPCR) to confirm aCGH-detected potentially clinically relevant imbalances. Only samples with DLRS <0.2 were tested for confirmation. aCGH results were confirmed in 102/118 cases (86.5%). A major element for non-confirmation was the dimension (and the probe coverage) of the putative aberration. Imbalances detected by 10 or less probes in aCGH assay were not confirmed in 11 out of 41 cases (26.8%), while those ones detected by 20 or more probes were always confirmed (46 cases). Among not confirmed imbalances, no statistical difference was found between deletions and duplication. Our data indicate that validation should be required for imbalances detected by less than 10 probes in aCGH assays.
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Affiliation(s)
| | - Nadia Passon
- Institute of Medical Genetics, Academic Hospital "Azienda Sanitaria Universitaria Integrata di Udine", Udine, Italy
| | - Silvia Burra
- Department of Medicine, University of Udine, Udine, Italy
| | - Eliana Demori
- Institute of Medical Genetics, Academic Hospital "Azienda Sanitaria Universitaria Integrata di Udine", Udine, Italy
| | - Patrizia Dello Russo
- Institute of Medical Genetics, Academic Hospital "Azienda Sanitaria Universitaria Integrata di Udine", Udine, Italy
| | - Giuseppe Damante
- Department of Medicine, University of Udine, Udine, Italy; Institute of Medical Genetics, Academic Hospital "Azienda Sanitaria Universitaria Integrata di Udine", Udine, Italy
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7
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Alesi V, Loddo S, Calì F, Orlando V, Genovese S, Ferretti D, Calacci C, Calvieri G, Falasca R, Ulgheri L, Drago F, Dallapiccola B, Baban A, Novelli A. A heterozygous, intragenic deletion of CNOT2 recapitulates the phenotype of 12q15 deletion syndrome. Am J Med Genet A 2019; 179:1615-1621. [PMID: 31145527 DOI: 10.1002/ajmg.a.61217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/10/2019] [Accepted: 05/13/2019] [Indexed: 01/19/2023]
Abstract
Only a few individuals with 12q15 deletion have been described, presenting with a disorder characterized by learning disability, developmental delay, nasal speech, and hypothyroidism. The smallest region of overlap for this syndrome was included in a genomic segment spanning CNOT2, KCNMB4, and PTPRB genes. We report on an additional patient harboring a 12q15 microdeletion encompassing only part of CNOT2 gene, presenting with a spectrum of clinical features overlapping the 12q15 deletion syndrome phenotype. We propose CNOT2 as the phenocritical gene for 12q15 deletion syndrome and its haploinsufficiency being associated with an autosomal dominant disorder, presenting with developmental delay, hypotonia, feeding problems, learning difficulties, nasal speech, skeletal anomalies, and facial dysmorphisms.
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Affiliation(s)
- Viola Alesi
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sara Loddo
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Calì
- Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Orlando
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniele Ferretti
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chiara Calacci
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giusy Calvieri
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Roberto Falasca
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lucia Ulgheri
- Department of Biomedical Sciences, Clinical Genetics Service, Azienda Ospedaliero-Universitaria, Sassari, Italy
| | - Fabrizio Drago
- Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Anwar Baban
- Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Department of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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8
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Uehara T, Takenouchi T, Yamaguchi Y, Daimon Y, Suzuki H, Sakaguchi Y, Kosaki K. CNOT2
as the critical gene for phenotypes of 12q15 microdeletion syndrome. Am J Med Genet A 2019; 179:659-662. [DOI: 10.1002/ajmg.a.61068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/06/2019] [Accepted: 01/23/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Tomoko Uehara
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
| | - Toshiki Takenouchi
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
- Department of Pediatrics; Keio University School of Medicine; Tokyo Japan
| | - Yu Yamaguchi
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
- Department of Clinial Genetics; Gunma Children's Medical Center; Gunma Japan
| | - Yumi Daimon
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
- Department of Pediatrics; Hino Municipal Hospital; Tokyo Japan
| | - Hisato Suzuki
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
| | - Yuri Sakaguchi
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
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9
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Alesi V, Loddo S, Grispo M, Riccio S, Montella AC, Dallapiccola B, Ulgheri L, Novelli A. Reassessment of the 12q15 deletion syndrome critical region. Eur J Med Genet 2017; 60:220-223. [DOI: 10.1016/j.ejmg.2017.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/28/2017] [Accepted: 01/29/2017] [Indexed: 01/05/2023]
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10
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Oliveira R, Pereira C, Melo JB, Mesquita S, Venâncio M, Carreira IM, Saraiva J. 12q21.2q22 deletion: a new patient. Am J Med Genet A 2015; 167A:1877-83. [PMID: 25845712 DOI: 10.1002/ajmg.a.37077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 03/12/2015] [Indexed: 11/08/2022]
Abstract
Interstitial deletions of long arm of chromosome 12 are rare, and the interstitial deletion 12q21.1q22 has been reported to the best of our knowledge in only four patients. Comparing the patients reported, a characteristic phenotypic pattern (facial features like prominent forehead, short and upturned nose, low set ears, and ectodermal abnormalities) can be identified. It has been suggested to be considered a deletion syndrome [Klein et al., (2005); Am J Med Genet 138:349-354]. We report on a 34-month-old girl, who was referred to our clinic at 6 months of age, presenting at birth with axial hypotonia, enlarged anterior fontanel, ventriculomegaly, dysmorphic facies (prominent forehead, sparse hair and eyebrows, short palpebral fissures), failure to thrive and development delay. Her cytogenetic study showed an interstitial deletion of the long arm of chromosome 12: 46,XX,del(12)(q21.1q22) redefined by array comparative genomic hybridization. We compare and review our patient with the four previously reported cases, plus one with a deletion with an overlap of the chromosomal region and phenotypic similarities. As far as we know our patient is the fourth reported with this cytogenetic abnormality. This additional report allows us to support a genotype-phenotype correlation for this chromosomal abnormality.
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Affiliation(s)
- Renata Oliveira
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Cristina Pereira
- Center for Child Development Luís Borges, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joana B Melo
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CIMAGO - Centro de Investigação em Meios Ambiente, Genética e Oncobiologia, Coimbra, Portugal
| | - Sandra Mesquita
- Paediatric Service, Centro Hospitalar Cova da Beira, Covilhã, Portugal
| | - Margarida Venâncio
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel Marques Carreira
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CIMAGO - Centro de Investigação em Meios Ambiente, Genética e Oncobiologia, Coimbra, Portugal
| | - Jorge Saraiva
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,CIMAGO - Centro de Investigação em Meios Ambiente, Genética e Oncobiologia, Coimbra, Portugal.,University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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11
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Wang R, Carter J, Lench N. Evaluation of real-time quantitative PCR as a standard cytogenetic diagnostic tool for confirmation of microarray (aCGH) results and determination of inheritance. Genet Test Mol Biomarkers 2013; 17:821-5. [PMID: 24024523 DOI: 10.1089/gtmb.2013.0284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIM To evaluate the use of real-time quantitative PCR (qPCR) as a diagnostic tool for follow up of abnormal microarray (aCGH) results. METHOD qPCR was performed on 207 samples with known aCGH results to detect chromosomal abnormality and determine the capability of qPCR. Eighty-four samples were processed and the results compared with the original aCGH result and with one or more of the alternative follow-up methods: aCGH, fluorescence in situ hybridization (FISH), or karyotyping. A separate cohort of 107 samples was used to determine critical threshold values for qPCR. A further 16 samples were assessed in reproducibility and sensitivity studies. RESULTS All qPCR findings were consistent with the original aCGH results, and qPCR was found to be a superior follow-up method compared to FISH and karyotyping. Critical threshold values were also determined from this study. CONCLUSION In this study, qPCR analysis identified all copy number changes. qPCR is an accurate, rapid, reliable, and inexpensive technique for confirming copy number changes, and for determining the inheritance of such abnormalities to aid interpretation of results. We also present the critical threshold values required for qPCR as a practical tool. This technique has now been successfully implemented as part of the clinical diagnostic service within our laboratory.
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Affiliation(s)
- Rubin Wang
- NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children , London, United Kingdom
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12
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Lopez E, Callier P, Cormier-Daire V, Lacombe D, Moncla A, Bottani A, Lambert S, Goldenberg A, Doray B, Odent S, Sanlaville D, Gueneau L, Duplomb L, Huet F, Aral B, Thauvin-Robinet C, Faivre L. Search for a gene responsible for Floating-Harbor syndrome on chromosome 12q15q21.1. Am J Med Genet A 2012; 158A:333-9. [PMID: 22247066 DOI: 10.1002/ajmg.a.34401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 10/19/2011] [Indexed: 12/17/2022]
Abstract
Floating-Harbor syndrome (FHS) is characterized by characteristic facial dysmorphism, short stature with delayed bone age, and expressive language delay. To date, the gene(s) responsible for FHS is (are) unknown and the diagnosis is only made on the basis of the clinical phenotype. The majority of cases appeared to be sporadic but rare cases following autosomal dominant inheritance have been reported. We identified a 4.7 Mb de novo 12q15-q21.1 microdeletion in a patient with FHS and intellectual deficiency. Pangenomic 244K array-CGH performed in a series of 12 patients with FHS failed to identify overlapping deletions. We hypothesized that FHS is caused by haploinsufficiency of one of the 19 genes or predictions located in the deletion found in our index patient. Since none of them appeared to be good candidate gene by their function, a high-throughput sequencing approach of the region of interest was used in eight FHS patients. No pathogenic mutation was found in these patients. This approach failed to identify the gene responsible for FHS, and this can be explained by at least four reasons: (i) our index patient could be a phenocopy of FHS; (ii) the disease may be clinically heterogeneous (since the diagnosis relies exclusively on clinical features), (iii) these could be genetic heterogeneity of the disease, (iv) the patient could carry a mutation in a gene located elsewhere. Recent descriptions of patients with 12q15-q21.1 microdeletions argue in favor of the phenocopy hypothesis.
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Affiliation(s)
- Estelle Lopez
- Equipe GAD, IFR Santé-STIC, Université de Bourgogne, Dijon, France
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Vergult S, Krgovic D, Loeys B, Lyonnet S, Liedén A, Anderlid BM, Sharkey F, Joss S, Mortier G, Menten B. Nasal speech and hypothyroidism are common hallmarks of 12q15 microdeletions. Eur J Hum Genet 2011; 19:1032-7. [PMID: 21505450 DOI: 10.1038/ejhg.2011.67] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The introduction of array CGH in clinical diagnostics has led to the discovery of many new microdeletion/microduplication syndromes. Most of them are rare and often present with a variable range of clinical anomalies. In this study we report three patients with a de novo overlapping microdeletion of chromosome bands 12q15q21.1. The deletions are ∼2.5 Mb in size, with a 1.34-Mb common deleted region containing six RefSeq genes. All three patients present with learning disability or developmental delay, nasal speech and hypothyroidism. In this paper we will further elaborate on the genotype-phenotype correlation associated with this deletion and compare our patients with previously reported cases.
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Affiliation(s)
- Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Adam MP, Mehta A, Knight L, Hall DE, Rossi MR. A family with a 1.17 Mb deletion of 12q12: refining genotype-phenotype correlation. Am J Med Genet A 2010; 152A:2394-8. [PMID: 20683996 DOI: 10.1002/ajmg.a.33570] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Margaret P Adam
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
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MLPA for confirmation of array CGH results and determination of inheritance. Mol Cytogenet 2010; 3:19. [PMID: 20942916 PMCID: PMC2964523 DOI: 10.1186/1755-8166-3-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 10/13/2010] [Indexed: 12/22/2022] Open
Abstract
Background Array CGH has recently been introduced into our laboratory in place of karyotype analysis for patients with suspected genomic imbalance. Results require confirmation to check sample identity, and analysis of parental samples to determine inheritance and thus assess the clinical significance of the abnormality. Here we describe an MLPA-based strategy for the follow-up of abnormal aCGH results. Results In the first 17 months of our MLPA-based aCGH follow-up service, 317 different custom MLPA probes for novel aCGH-detected abnormalities were developed for inheritance studies in 164 families. In addition, 110 samples were tested for confirmation of aCGH-detected abnormalities in common syndromic or subtelomeric regions using commercial MLPA kits. Overall, a total of 1215 samples have been tested by MLPA. A total of 72 de novo abnormalities were confirmed. Conclusions Confirmation of aCGH-detected abnormalities and inheritance of these abnormalities are essential for accurate diagnosis and interpretation of aCGH results. The development of a new service utilising custom made MLPA probes and commercial MLPA kits for follow-up studies of array CGH results has been found to be efficient and flexible in our laboratory.
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