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Silveira HG, Steiner CE, Toccoli G, Angeloni LL, Heleno JL, Spineli-Silva S, dos Santos AM, Vieira TP, Melaragno MI, Gil-da-Silva-Lopes VL. Variants in KMT2A in Three Individuals with Previous Suspicion of 22q11.2 Deletion Syndrome. Genes (Basel) 2024; 15:211. [PMID: 38397201 PMCID: PMC10888166 DOI: 10.3390/genes15020211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The condition known as 22q11.2 deletion syndrome (MIM #188400) is a rare disease with a highly variable clinical presentation including more than 180 features; specific guidelines for screening individuals have been used to support clinical suspicion before confirmatory tests by Brazil's Craniofacial Project. Of the 2568 patients listed in the Brazilian Database on Craniofacial Anomalies, 43 individuals negative for the 22q11.2 deletion syndrome were further investigated through whole-exome sequencing. Three patients (6.7%) presented with heterozygous pathogenic variants in the KMT2A gene, including a novel variant (c.6158+1del) and two that had been previously reported (c.173dup and c.3241C>T); reverse phenotyping concluded that all three patients presented features of Wiedemann-Steiner syndrome, such as neurodevelopmental disorders and dysmorphic facial features (n = 3), hyperactivity and anxiety (n = 2), thick eyebrows and lower-limb hypertrichosis (n = 2), congenital heart disease (n = 1), short stature (n = 1), and velopharyngeal insufficiency (n = 2). Overlapping features between 22q11.2 deletion syndrome and Wiedemann-Steiner syndrome comprised neuropsychiatric disorders and dysmorphic characteristics involving the eyes and nose region; velopharyngeal insufficiency was seen in two patients and is an unreported finding in WDSTS. Therefore, we suggest that both conditions should be included in each other's differential diagnoses.
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Affiliation(s)
- Henrique Garcia Silveira
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (Unifesp), São Paulo 04023-062, Brazil; (H.G.S.); (G.T.); (M.I.M.)
| | - Carlos Eduardo Steiner
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Giovana Toccoli
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (Unifesp), São Paulo 04023-062, Brazil; (H.G.S.); (G.T.); (M.I.M.)
| | - Luise Longo Angeloni
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Júlia Lôndero Heleno
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Samira Spineli-Silva
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Ana Mondadori dos Santos
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
- Faculdade São Leopoldo Mandic (SLMandic), Campinas 13045-755, Brazil
| | - Társis Paiva Vieira
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
| | - Maria Isabel Melaragno
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (Unifesp), São Paulo 04023-062, Brazil; (H.G.S.); (G.T.); (M.I.M.)
| | - Vera Lúcia Gil-da-Silva-Lopes
- Genética Médica e Medicina Genômica, Departamento de Medicina Translacional, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (Unicamp), Campinas 13083-970, Brazil; (C.E.S.); (L.L.A.); (J.L.H.); (S.S.-S.); (A.M.d.S.); (T.P.V.)
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Dincsoy Bir F, Silan F, Velickovic J, Berkay Akcan M, Ozdemir O. A New Case of Rare Microdeletion 10q22.3q23 along with Mosaic Klinefelter Syndrome Associated with Facial Dysmorphic Finding, Atrial Ventricular Septal Defect, and Motor Retardation. Mol Syndromol 2022; 13:254-260. [DOI: 10.1159/000519965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/28/2021] [Indexed: 11/19/2022] Open
Abstract
The chromosome 10q22.3q23.2 deletion syndrome is characterized by craniofacial dysmorphic features, developmental delay, congenital heart defect, and hand/foot abnormalities. In this study, we report a patient carrying a microdeletion of 7.5 Mb at 10q22.3q23.2 and in addition a mosaicism mos 47,XXY[47]/46,XY[23].This male patient was 3 years and 3 months years old at the time of genetic evaluation. Atrial ventricular septal defect (AVSD), mild hypotonia, torticollis, and left-sided club foot were noticed after birth. The boy had surgical correction of the AVSD and the club foot. His dysmorphic features were frontal bossing, overfolded ear helix, hypertelorism, epicanthal folds, broad base of nose, flat nasal bridge, full cheeks, thick lips, micrognathia, and joint hyperextensibility. His speech/language development was delayed. Klinefelter syndrome is one of the most common congenital chromosomal abnormalities, but usually it is detected in puberty or in adulthood when reproductive failure occurs. Deletions in the 10q22.3q23.2 region are rare, and previously only a few numbers of cases were described with this microdeletion, but none of them together with Klinefelter syndrome and it could be associated with our case clinical features. The new case described will improve understanding the phenotype associated with 10q22.3q23.2 microdeletions. By presenting this case, we aimed to improve the understanding of the phenotype caused by the rare 10q22.3q23.2 deletion and to show the rare coexistence of this deletion with Klinefelter syndrome.
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He X, Shen H, Fu H, Feng C, Liu Z, Jin Y, Mao J. Reduced anogenital distance, hematuria and left renal hypoplasia in a patient with 13q33.1-34 deletion: case report and literature review. BMC Pediatr 2020; 20:327. [PMID: 32616040 PMCID: PMC7330938 DOI: 10.1186/s12887-020-02205-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/12/2020] [Indexed: 12/02/2022] Open
Abstract
Background 13q33–q34 microdeletions are rare chromosomal aberrations associated with a high risk of developmental disability, facial dysmorphism, cardiac defects and other malformation of organs. It is necessary to collect and report evidence of this rare chromosome mutation to improve the prognosis of this rare disease. Case presentation We report a patient harboring an 11.56 Mb microdeletion at 13q33.1–34 region, which contains about 30 OMIM genes. Besides the common clinical manifestations such as facial dysmorphism, developmental delay, intellectual disability, epilepsy, and congenital heart disease, she also suffered from a reduced anogenital distance, hematuria and left renal hypoplasia. Most related cases were characterized by facial deformity and heart defects, but there were few reports on renal malformation, especially regarding renal hypoplasia with hematuria. Conclusion We have reported a patient suffering from a reduced anogenital distance, hematuria and left renal hypoplasia. A de novo 11.56 Mb deletion ranging from 13q33.1 to 13q34 (Chr13:103542220–115,106,996) was found by SNP-array analysis. It might be the first time for hematuria and renal hypoplasia to be reported as symptoms of 13q33-q34 deletion syndrome Neurodevelopmental disability, heart defects and urogenital/anorectal anomalies may be resulted from common or overlapping regions of deletion in chromosome bands 13q33.1-q34 and may share a common molecular mechanism.
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Affiliation(s)
- Xue He
- Department of Nephrology, National Clinical Research Center For Child Health, The Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, Zhejiang Province, 310003, P.R. China
| | - Huijun Shen
- Department of Nephrology, National Clinical Research Center For Child Health, The Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, Zhejiang Province, 310003, P.R. China
| | - Haidong Fu
- Department of Nephrology, National Clinical Research Center For Child Health, The Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, Zhejiang Province, 310003, P.R. China
| | - Chunyue Feng
- Department of Nephrology, National Clinical Research Center For Child Health, The Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, Zhejiang Province, 310003, P.R. China
| | - Zhixia Liu
- Department of Nephrology, National Clinical Research Center For Child Health, The Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, Zhejiang Province, 310003, P.R. China
| | - Yanyan Jin
- Department of Nephrology, National Clinical Research Center For Child Health, The Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, Zhejiang Province, 310003, P.R. China
| | - Jianhua Mao
- Department of Nephrology, National Clinical Research Center For Child Health, The Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, Zhejiang Province, 310003, P.R. China.
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Palumbo O, Palumbo P, Di Muro E, Cinque L, Petracca A, Carella M, Castori M. A Private 16q24.2q24.3 Microduplication in a Boy with Intellectual Disability, Speech Delay and Mild Dysmorphic Features. Genes (Basel) 2020; 11:genes11060707. [PMID: 32604767 PMCID: PMC7349372 DOI: 10.3390/genes11060707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/03/2022] Open
Abstract
No data on interstitial microduplications of the 16q24.2q24.3 chromosome region are available in the medical literature and remain extraordinarily rare in public databases. Here, we describe a boy with a de novo 16q24.2q24.3 microduplication at the Single Nucleotide Polymorphism (SNP)-array analysis spanning ~2.2 Mb and encompassing 38 genes. The patient showed mild-to-moderate intellectual disability, speech delay and mild dysmorphic features. In DECIPHER, we found six individuals carrying a “pure” overlapping microduplication. Although available data are very limited, genomic and phenotype comparison of our and previously annotated patients suggested a potential clinical relevance for 16q24.2q24.3 microduplication with a variable and not (yet) recognizable phenotype predominantly affecting cognition. Comparing the cytogenomic data of available individuals allowed us to delineate the smallest region of overlap involving 14 genes. Accordingly, we propose ANKRD11, CDH15, and CTU2 as candidate genes for explaining the related neurodevelopmental manifestations shared by these patients. To the best of our knowledge, this is the first time that a clinical and molecular comparison among patients with overlapping 16q24.2q24.3 microduplication has been done. This study broadens our knowledge of the phenotypic consequences of 16q24.2q24.3 microduplication, providing supporting evidence of an emerging syndrome.
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Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies. Biochem Genet 2019; 58:74-101. [PMID: 31273557 DOI: 10.1007/s10528-019-09931-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
Abstract
Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic information over classical cytogenetics for identifying genomic imbalances in a pediatric cohort with idiopathic DD, DF, or CA. One hundred sixty-nine patients were offered cytogenetics and CMA simultaneously for etiological diagnosis of DD (n = 67), DF (n = 52) and CA (n = 50). CMA could identify additional, clinically significant anomalies as compared with cytogenetics. CMA detected 61 CNVs [21 (34.4%) pathogenic CNVs, 37 (60.7%) variants of uncertain clinical significance and 3 (4.9%) benign CNVs] in 44 patients. CMA identified one or more ROH in 116/169 (68.6%) patients. When considering pathogenic CNVs and aneuploidies as positive findings, 9/169 (5.3%) received a genetic diagnosis from cytogenetics, while 25/169 (14.8%) could have a genetic diagnosis from CMA. The identification of ROH was clinically significant in two cases (2/169), thereby, adding 1.2% to the diagnostic yield of CMA (16% vs. 5.3%, p < 0.001). CMA uncovers additional genetic diagnoses over cytogenetics, thereby, offering a much higher diagnostic yield. Our findings convincingly demonstrate the additive diagnostic value of clinically significant ROH identified during CMA testing, highlighting the need for careful clinical interpretation of these ROH.
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Chen C, Heng EYH, Lim AST, Lau LC, Lim TH, Wong GC, Tien SL. Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay. Int J Lab Hematol 2019; 41:561-571. [PMID: 31112375 DOI: 10.1111/ijlh.13052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Conventional cytogenetics (CC) is important in diagnosis, therapy, monitoring of post-transplant bone marrow, and prognosis assessment of acute lymphoblastic leukemia (ALL). However, due to the nature of ALL, CC often encounters difficulties of complex karyotype, poor chromosome morphology, low mitotic index, or normal cells dividing only. In contrast, chromosomal microarray analysis (CMA) showed a specificity >99% and a sensitivity of 100% in chronic lymphocytic leukemia (CLL) patients. Here, we report our experience with CMA on adult ALL patients. METHODS Thirty-three bone marrow/blood samples from ALL patients (aged 18-79 years, median 44) at diagnosis/relapse, analyzed by CC and/or fluorescence in situ hybridization (FISH), were recruited. Chromosomal microarray analysis results were compared with CC. Fluorescence in situ hybridization analysis, if available, was applied when there was a discrepancy. RESULTS Copy-neutral loss-of-heterozygosity (CN-LOH) was found in 8 cases (24.2%). Only CN-LOH at 9p was recurrent (3 cases, 9.1%). Copy number alterations (CNAs) were detected in 6 of 9 cases (66.7%) with normal karyotypes, in 3 of 5 cases (60.0%) with sole "balanced" translocations, and in 18 of 19 cases (94.7%) with complex karyotypes. Common CNAs involved CDKN2A/2B (30.3%), IKZF1 (27.3%), PAX5 (9.1%), RB1 (9.1%), BTG1 (6.7%), and ETV6 (6.7%), which regulate cell cycle, B lymphopoiesis, or act as tumor suppressors in ALL. Copy number alteration detection rate by CMA was 81.8% (27 of 33 cases) as compared to 57.6% (19 of 33 cases) by CC. CONCLUSION Incorporation of CMA as a routine clinical test at the time of diagnosis/relapse, in conjunction with CC and/or FISH, is highly recommended.
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Affiliation(s)
- Chuanfei Chen
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Evelyn Yee Hsieh Heng
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Alvin Soon Tiong Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Lai Ching Lau
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Tse Hui Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Gee Chuan Wong
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Sim Leng Tien
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore.,Department of Haematology, Singapore General Hospital, Singapore, Singapore
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Yanagishita T, Yamamoto-Shimojima K, Nakano S, Sasaki T, Shigematsu H, Imai K, Yamamoto T. Phenotypic features of 1q41q42 microdeletion including WDR26 and FBXO28 are clinically recognizable: The first case from Japan. Brain Dev 2019; 41:452-455. [PMID: 30635136 DOI: 10.1016/j.braindev.2018.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/23/2018] [Accepted: 12/26/2018] [Indexed: 01/11/2023]
Abstract
1q41q42 microdeletion syndrome has been established in 2007. Since then, more than 17 patients have been reported so far. The reported deletions showed random breakpoints and deletion regions are aligned as roof tiles. Patients with 1q41q42 microdeletion syndrome show intellectual disability, seizures, and distinctive features. Many genotype-phenotype correlation studies have been performed and some genes included in this region have been suggested as potential candidate genes. Recently, de novo variants in WDR26 and FBXO28 were identified in patients who showed consistent phenotypes with 1q41q42 microdeletion syndrome. Thus, both genes are now considered as the genes possibly responsible for 1q41q42 microdeletion syndrome. Here, the first case of a Japanese patient with a de novo 1q41q42 microdeletion is reported. Owing to the distinctive features, this syndrome would be clinically recognizable.
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Affiliation(s)
- Tomoe Yanagishita
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Yamamoto-Shimojima
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan
| | - Sayaka Nakano
- Department of Pediatrics, National Hospital Organization Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Testuya Sasaki
- Department of Pediatrics, Iwate Prefectural Chubu Hospital, Kitakami, Japan
| | - Hideo Shigematsu
- Department of Pediatrics, National Hospital Organization Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Katsumi Imai
- Department of Pediatrics, National Hospital Organization Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan.
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Arora V, Aggarwal S, Bijarnia S, Lall M, Joshi A, Dua-Puri R, Arora U, Verma I. Extending the Phenotype and Identification of a Novel Candidate Gene for Immunodeficiency in 5q11 Microdeletion Syndrome. Mol Syndromol 2018; 9:312-318. [PMID: 30800048 DOI: 10.1159/000494995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2018] [Indexed: 11/19/2022] Open
Abstract
Array CGH has led to the delineation of innumerable microdeletion syndromes. We present a patient with a 7-Mb deletion at 5q11.2 with previously unreported features, such as immunodeficiency, asymmetry of hands and feet, joint laxity, and agenesis of corpus callosum. The clinical features of this patient are compared with 13 patients reported previously. A common critical region (CCR) of 1.4 Mb (54-55.4 Mb) is defined in all cases including the present one. Of the 14 genes present in CCR, IL6ST is proposed to be the candidate gene for immunodeficiency observed in some of these patients. IL6ST encodes gp130, a signal transduction protein for various interleukins and cytokines. It is involved in the generation of both T and B lymphocytes as well as the production of acute-phase reactants. Microdeletion 5q11.2 should be considered as a recognisable syndrome based on the common phenotype and the novel features described.
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Affiliation(s)
- Veronica Arora
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Shruti Aggarwal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Meena Lall
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Anju Joshi
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua-Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Umang Arora
- All India Institute of Medical Sciences, New Delhi, India
| | - Ishwar Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
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Multiplex ligation dependent probe amplification - A useful, fast and cost-effective method for identification of small supernumerary marker chromosome in children with developmental delay and congenital heart defect. REV ROMANA MED LAB 2018. [DOI: 10.2478/rrlm-2018-0032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abstract
Small supernumerary marker chromosome (sSMC) is a rare chromosomal abnormality and is detected in about 0.3% in cases with multiple congenital anomalies (MCA) and/or developmental delay. Different techniques for investigation of cases with MCA and/or developmental delay are available ranging from karyotyping to molecular cytogenetic technique and ultimately multiplex ligation dependent probe amplification (MLPA). Here we present a patient with multiple congenital anomalies for which classical cytogenetic technique was used as a first step in diagnosis and the results being confirmed by MLPA. The karyotype disclosed a sSMC considered to be a fragment of chromosome 22. The MLPA analysis using SALSA MLPA probemix P064-C2 Microdeletion Syndromes-1B confirmed the karyotype results, and according to the manufacturer’s recommendation we performed another confirmation analysis with MLPA probemix P311-B1 Congenital Heart Disease and MLPA probemix P250-B2 DiGeorge. We also suspected an Emanuel syndrome and performed another MLPA analysis with SALSA MLPA probemix P036-E3 Subtelomeres Mix 1 and probemix P070-B3 Subtelomeres Mix 2B for investigation of subtelomeric region that revealed a duplication of 11q25 region and the confirmation was performed using SALSA MLPA probemix P286-B2 Human Telomere-11.
In conclusion, we consider that MLPA is a valuable method for identification of sSMC in children with developmental delay and congenital anomalies. Genetic diagnosis using different molecular techniques, such as MLPA, for increasing accuracy in identification of chromosomal structural aberrations has an important role in clinical diagnosis and in genetic counselling and our case explain the importance of using a specific laboratory technique for each stage of diagnosis.
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Engels H. Strukturelle Chromosomenstörungen bei Intelligenzminderung. MED GENET-BERLIN 2018. [DOI: 10.1007/s11825-018-0200-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Zusammenfassung
Strukturelle und numerische Chromosomenstörungen gehören zu den häufigen Ursachen der Intelligenzminderung und psychomotorischen Entwicklungsstörung. Die große Heterogenität der Intelligenzminderung spiegelt sich auch in der Vielfalt möglicher Aberrationstypen und ursächlicher Chromosomenregionen wider. Die konventionelle lichtmikroskopische Zytogenetik kann hierbei u. a. strukturelle Aberrationen mit Größen über ca. 5–10 Megabasenpaaren (Mb) auch in Form kleinerer Mosaike nachweisen und diese im Genom lokalisieren. Durch Fluoreszenz-in situ-Hybridisierung können bei klinischem Verdacht gezielt auch deutlich kleinere Aberrationen, z. B. Mikrodeletionen, detektiert werden. Chromosomale Mikroarrays (CMA) detektieren dank ihrer besseren Auflösung, die bis deutlich unter 0,1 Mb reichen kann, genomweit submikroskopische Mikrodeletionen und Mikroduplikationen, machen jedoch bei Duplikationen keine Aussage zu deren genomischer Lokalisation und können meist niedriggradige Mosaike unter 20 % kaum nachweisen. Zytogenetik und CMA ergänzen sich aufgrund ihrer unterschiedlichen Fähigkeiten und weisen einschließlich der Trisomie 21 jeweils in ungefähr 15 % der Patienten mit Intelligenzminderung ursächliche Chromosomenaberrationen nach. Sie stellen damit neben aktuellen Sequenzierungstechniken ein wichtiges Element der humangenetischen Ursachenabklärung bei Intelligenzminderung dar. Typische chromosomale Aberrationstypen werden beispielhaft besprochen und in das heutige Gesamtbild eingeordnet.
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Affiliation(s)
- Hartmut Engels
- Aff1 0000 0000 8786 803X grid.15090.3d Institut für Humangenetik Universitätsklinikum Bonn Sigmund-Freud-Str. 25 53105 Bonn Deutschland
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Ceroni JRM, Dutra RL, Honjo RS, Llerena JC, Acosta AX, Medeiros PFV, Galera MF, Zanardo ÉA, Piazzon FB, Dias AT, Novo-Filho GM, Montenegro MM, Madia FAR, Bertola DR, de Melo JB, Kulikowski LD, Kim CA. A Multicentric Brazilian Investigative Study of Copy Number Variations in Patients with Congenital Anomalies and Intellectual Disability. Sci Rep 2018; 8:13382. [PMID: 30190605 PMCID: PMC6127201 DOI: 10.1038/s41598-018-31754-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/21/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic imbalances are the most common cause of congenital anomalies (CA) and intellectual disability (ID). The aims of this study were to identify copy number variations (CNVs) in 416 patients with CA and ID from 5 different genetics centers within 4 different states by using the Multiplex Ligation-dependent Probe Amplification (MLPA) technique and to apply the chromosomal microarray (CMA) methodology in selected cases. The samples were analyzed by MLPA kits P064, P036, P070 and P250. Positive results were found in 97/416 (23.3%) patients. CMA was applied in 14 selected cases. In 6/14 (42.85%) patients, CMA detected other copy number variations not detected by the MLPA studies. Although CMA is indispensable for genotype refinement, the technique is still unfeasible in some countries as a routine analysis due to economic and technical limitations. In these cases, clinical evaluation followed by karyotyping and MLPA analysis is a helpful and affordable solution for diagnostic purposes.
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Affiliation(s)
- J R M Ceroni
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil.
| | - R L Dutra
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - R S Honjo
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil
| | - J C Llerena
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil
| | - A X Acosta
- Universidade Federal da Bahia, Salvador, BA, Brazil
| | - P F V Medeiros
- Universidade Federal de Campina Grande, Campina Grande, PB, Brazil
| | - M F Galera
- Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - É A Zanardo
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - F B Piazzon
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - A T Dias
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - G M Novo-Filho
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - M M Montenegro
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - F A R Madia
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - D R Bertola
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil.,Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil., São Paulo, SP, Brazil
| | - J B de Melo
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Faculdade de Medicina, Universidade de Coimbra, CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - L D Kulikowski
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - C A Kim
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil
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12
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Maini I, Ivanovski I, Djuric O, Caraffi SG, Errichiello E, Marinelli M, Franchi F, Bizzarri V, Rosato S, Pollazzon M, Gelmini C, Malacarne M, Fusco C, Gargano G, Bernasconi S, Zuffardi O, Garavelli L. Prematurity, ventricular septal defect and dysmorphisms are independent predictors of pathogenic copy number variants: a retrospective study on array-CGH results and phenotypical features of 293 children with neurodevelopmental disorders and/or multiple congenital anomalies. Ital J Pediatr 2018; 44:34. [PMID: 29523172 PMCID: PMC5845186 DOI: 10.1186/s13052-018-0467-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/21/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician. METHOD We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016. The aim of the study was to analyze clinical and molecular cytogenetic data in order to identify what elements could be useful to interpret unknown or poorly described aberrations. Comparison of phenotype and cytogenetic characteristics through univariate analysis and multivariate logistic regression was performed. RESULTS Copy number variations (CNVs) with a frequency < 1% were detected in 225 patients of the total sample, while 68 patients presented only variants with higher frequency (heterozygous deletions or amplification) and were considered to have negative aCGH. Proved pathogenic CNVs were detected in 70 patients (20.6%). Delayed psychomotor development, intellectual disability, intrauterine growth retardation (IUGR), prematurity, congenital heart disease, cerebral malformations and dysmorphisms correlated to reported pathogenic CNVs. Prematurity, ventricular septal defect and dysmorphisms remained significant predictors of pathogenic CNVs in the multivariate logistic model whereas abnormal EEG and limb dysmorphisms were mainly detected in the group with likely pathogenic VOUS. A flow-chart regarding the care for patients with NDD and/or MCA and/or dysmorphisms and the interpretation of aCGH has been made on the basis of the data inferred from this study and literature. CONCLUSION Our work contributes to make the investigative process of CNVs more informative and suggests possible directions in aCGH interpretation and phenotype correlation.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Adolescent
- Adult
- Child
- Child, Preschool
- Comparative Genomic Hybridization/methods
- DNA Copy Number Variations
- Facies
- Female
- Genetic Testing
- Heart Septal Defects, Ventricular/diagnosis
- Heart Septal Defects, Ventricular/genetics
- Humans
- Infant
- Infant, Newborn
- Infant, Premature, Diseases/diagnosis
- Infant, Premature, Diseases/genetics
- Male
- Muscular Atrophy/diagnosis
- Muscular Atrophy/genetics
- Neurodevelopmental Disorders/diagnosis
- Neurodevelopmental Disorders/genetics
- Phenotype
- Retrospective Studies
- Young Adult
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Affiliation(s)
- I. Maini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - I. Ivanovski
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - O. Djuric
- Institute of Epidemiology, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - S. G. Caraffi
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - E. Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - M. Marinelli
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - F. Franchi
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - V. Bizzarri
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Rosato
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Pollazzon
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - C. Gelmini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Malacarne
- Division of Medical Genetics, Galliera Hospital, Genoa, Italy
| | - C. Fusco
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - G. Gargano
- Neonatal Intensive Care Unit (NICU), Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Bernasconi
- Former Director Pediatric Department, University of Parma, Parma, Italy
| | - O. Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - L. Garavelli
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Santa Maria Nuova Hospital, viale Risorgimento 80, 42123 Reggio Emilia, Italy
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13
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Iourov IY, Zelenova MA, Vorsanova SG, Voinova VV, Yurov YB. 4q21.2q21.3 Duplication: Molecular and Neuropsychological Aspects. Curr Genomics 2018; 19:173-178. [PMID: 29606904 PMCID: PMC5850505 DOI: 10.2174/1389202918666170717161426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/20/2016] [Accepted: 01/20/2017] [Indexed: 12/15/2022] Open
Abstract
During the last decades, a large amount of newly described microduplications and microdeletions associated with intellectual disability (ID) and related neuropsychiatric diseases have been discovered. However, due to natural limitations, a significant part of them has not been the focus of multidisciplinary approaches. Here, we address previously undescribed chromosome 4q21.2q21.3 microduplication for gene prioritization, evaluation of cognitive abilities and estimation of genomic mechanisms for brain dysfunction by molecular cytogenetic (cytogenomic) and gene expression (meta-) analyses as well as for neuropsychological assessment. We showed that duplication at 4q21.2q21.3 is associated with moderate ID, cognitive deficits, developmental delay, language impairment, memory and attention problems, facial dysmorphisms, congenital heart defect and dentinogenesis imperfecta. Gene-expression meta-analysis prioritized the following genes: ENOPH1, AFF1, DSPP, SPARCL1, and SPP1. Furthermore, genotype/phenotype correlations allowed the attribution of each gene gain to each phenotypic feature. Neuropsychological testing showed visual-perceptual and fine motor skill deficits, reduced attention span, deficits of the nominative function and problems in processing both visual and aural information. Finally, emerging approaches including molecular cytogenetic, bioinformatic (genome/epigenome meta-analysis) and neuropsychological methods are concluded to be required for comprehensive neurological, genetic and neuropsychological descriptions of new genomic rearrangements/diseases associated with ID.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, Ministry of Health, Moscow, Russian Federation
| | - Maria A Zelenova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Svetlana G Vorsanova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Victoria V Voinova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Yuri B Yurov
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
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14
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16p11.2 transcription factor MAZ is a dosage-sensitive regulator of genitourinary development. Proc Natl Acad Sci U S A 2018; 115:E1849-E1858. [PMID: 29432158 DOI: 10.1073/pnas.1716092115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genitourinary (GU) birth defects are among the most common yet least studied congenital malformations. Congenital anomalies of the kidney and urinary tract (CAKUTs) have high morbidity and mortality rates and account for ∼30% of structural birth defects. Copy number variation (CNV) mapping revealed that 16p11.2 is a hotspot for GU development. The only gene covered collectively by all of the mapped GU-patient CNVs was MYC-associated zinc finger transcription factor (MAZ), and MAZ CNV frequency is enriched in nonsyndromic GU-abnormal patients. Knockdown of MAZ in HEK293 cells results in differential expression of several WNT morphogens required for normal GU development, including Wnt11 and Wnt4. MAZ knockdown also prevents efficient transition into S phase, affects transcription of cell-cycle regulators, and abrogates growth of human embryonic kidney cells. Murine Maz is ubiquitously expressed, and a CRISPR-Cas9 mouse model of Maz deletion results in perinatal lethality with survival rates dependent on Maz copy number. Homozygous loss of Maz results in high penetrance of CAKUTs, and Maz is haploinsufficient for normal bladder development. MAZ, once thought to be a simple housekeeping gene, encodes a dosage-sensitive transcription factor that regulates urogenital development and contributes to both nonsyndromic congenital malformations of the GU tract as well as the 16p11.2 phenotype.
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15
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Palumbo P, Accadia M, Leone MP, Palladino T, Stallone R, Carella M, Palumbo O. Clinical and molecular characterization of an emerging chromosome 22q13.31 microdeletion syndrome. Am J Med Genet A 2017; 176:391-398. [PMID: 29193617 DOI: 10.1002/ajmg.a.38559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 11/05/2022]
Abstract
Microdeletion of chromosome 22q13.31 is a very rare condition. Fourteen patients have been annotated in public databases but, to date, a clinical comparison has not been done and, consequently, a specific phenotype has not been delineated yet. We describe a patient showing neurodevelopmental disorders, dysmorphic features, and multiple congenital anomalies in which SNP array analysis revealed an interstitial 3.15 Mb de novo microdeletion in the 22q13.31 region encompassing 21 RefSeq genes and seven non-coding microRNAs. To perform an accurate phenotype characterization, clinical features observed in previously reported cases of 22q13.31 microdeletions were reviewed and compared to those observed in our patient. To the best of our knowledge, this is the first time that a comparison between patients carrying overlapping 22q13.31 deletions has been done. This comparison allowed us to identify a distinct spectrum of clinical manifestations suggesting that patients with a de novo interstitial microdeletion involving 22q13.31 have an emerging syndrome characterized by developmental delay/intellectual disability, speech delay/language disorders, behavioral problems, hypotonia, urogenital, and hands/feet anomalies. The microdeletion identified in our patient is the smallest reported so far and, for this reason, useful to perform a detailed genotype-phenotype correlation. In particular, we propose the CELSR1, ATXN10, FBLN1, and UPK3A as candidate genes in the onset of the main clinical features of this contiguous gene syndrome. Thus, the patient reported here broadens our knowledge of the phenotypic consequences of 22q13.31 microdeletions facilitating genotype-phenotype correlations. Additional cases are needed to corroborate our hypothesis and confirm genotype-phenotype correlations of this emerging syndrome.
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Affiliation(s)
- Pietro Palumbo
- Divisionof Medical Genetics, Poliambulatorio "Giovanni Paolo II," IRCCSCasa Sollievo della Sofferenza, Viale Padre Pio, San Giovanni Rotondo FG, Italy
| | - Maria Accadia
- Divisionof Medical Genetics, Poliambulatorio "Giovanni Paolo II," IRCCSCasa Sollievo della Sofferenza, Viale Padre Pio, San Giovanni Rotondo FG, Italy.,Medical Genetics Service, Hospital "Cardinale G. Panico," Via San Pio X n°4, Tricase, Italy
| | - Maria P Leone
- Divisionof Medical Genetics, Poliambulatorio "Giovanni Paolo II," IRCCSCasa Sollievo della Sofferenza, Viale Padre Pio, San Giovanni Rotondo FG, Italy.,Department of Soil, Plant, and Food Science, University of Bari "Aldo Moro,", Bari, Italy
| | - Teresa Palladino
- Divisionof Medical Genetics, Poliambulatorio "Giovanni Paolo II," IRCCSCasa Sollievo della Sofferenza, Viale Padre Pio, San Giovanni Rotondo FG, Italy
| | - Raffaella Stallone
- Divisionof Medical Genetics, Poliambulatorio "Giovanni Paolo II," IRCCSCasa Sollievo della Sofferenza, Viale Padre Pio, San Giovanni Rotondo FG, Italy
| | - Massimo Carella
- Divisionof Medical Genetics, Poliambulatorio "Giovanni Paolo II," IRCCSCasa Sollievo della Sofferenza, Viale Padre Pio, San Giovanni Rotondo FG, Italy
| | - Orazio Palumbo
- Divisionof Medical Genetics, Poliambulatorio "Giovanni Paolo II," IRCCSCasa Sollievo della Sofferenza, Viale Padre Pio, San Giovanni Rotondo FG, Italy
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16
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Coelho Molck M, Simioni M, Paiva Vieira T, Paoli Monteiro F, Gil-da-Silva-Lopes VL. A New Case of the Rare 10q22.3q23.2 Microdeletion Flanked by Low-Copy Repeats 3/4. Mol Syndromol 2017; 8:161-167. [PMID: 28588438 DOI: 10.1159/000469965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2017] [Indexed: 01/07/2023] Open
Abstract
Deletions in the 10q22.3q23.2 region are rare and mediated by 2 low-copy repeats (LCRs 3 and 4). These deletions have already been recognized as the 10q22q23 deletion syndrome. The phenotype associated with this condition is rather uncharacteristic, and most common features are craniofacial dysmorphisms and developmental delay. We describe a boy with craniofacial dysmorphic features, developmental delay, tetralogy of Fallot, hand/foot abnormalities, and recurrent respiratory tract infections. Chromosomal microarray analysis disclosed a 7.8-Mb microdeletion at 10q22.3q23.2, flanked by LCRs 3/4, and an additional 16q12.1 microdeletion of 189 kb. This article reviews the clinical signs of reported cases with similar deletions and compares them with our patient, contributing to a better understanding of genotype-phenotype correlation.
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Affiliation(s)
- Miriam Coelho Molck
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Milena Simioni
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Társis Paiva Vieira
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fabíola Paoli Monteiro
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Vera L Gil-da-Silva-Lopes
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
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17
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Sonmez FM, Uctepe E, Aktas D, Alikasifoglu M. Microdeletion of chromosome 1q21.3 in fraternal twins is associated with mental retardation, microcephaly, and epilepsy. Intractable Rare Dis Res 2017; 6:61-64. [PMID: 28357185 PMCID: PMC5359357 DOI: 10.5582/irdr.2016.01075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Reported here are twins, both of whom have a 1q21.3 microdeletion and who exhibit key features common to previously reported cases such as microcephaly and developmental delay. However, some clinical findings and deleted genes differed from those in previously reported cases. The karyotype was normal 46, XX for both of the twins. Array comparative genomic hybridization (CGH) identified a 2.6 Mb deletion on chromosome 1q21.3 (chr1: 153,514,121-156,171,335 bp) in case 1 and a 1.6 Mb deletion on chromosome 1q21.3 (chr1: 154,748,365-156,358,923 bp) in case 2. The deleted region includes DPM3, MUC1, GBA, PKLR, RIT1, and LAMTOR2 in both siblings. To the extent known, this is the second report of a 1q21.3 microdeletion in a family with mental retardation, developmental delay, seizures, and some dysmorphic features, thus expanding the phenotypic spectrum.
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Affiliation(s)
- Fatma Mujgan Sonmez
- Developmental Child Neurology Association, Ankara, Turkey
- Address correspondence to: Dr. Fatma Mujgan Sonmez, Developmental Child Neurology Association, Tunalı Hilmi Caddesi, Buğday Sokak. Kozlar İşhanı No:6/28, Kavaklıdere/Ankara, Turkey. E-mail:
| | - Eyyup Uctepe
- Department of Medical Genetics, Health Sciences University, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Dilek Aktas
- Damagen Genetic Diagnostic Center, Ankara, Turkey
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18
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Array comparative genomic hybridization and genomic sequencing in the diagnostics of the causes of congenital anomalies. J Appl Genet 2016; 58:185-198. [PMID: 27858254 DOI: 10.1007/s13353-016-0376-z] [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: 08/26/2016] [Revised: 10/19/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
The aim of this review is to provide the current state of knowledge about the usefulness of modern genetic technologies in uncovering the causality of isolated and multiple congenital anomalies. Array comparative genomic hybridization and next-generation sequencing have revolutionized the clinical approach to patients with these phenotypes. Both technologies enable early diagnosis, especially in clinically challenging newborn populations, and help to uncover genetic defects associated with various phenotypes. The application of both complementary methods could assist in identifying many variants that may simultaneously be involved in the development of a number of isolated or multiple congenital anomalies. Both technologies carry serious variant misinterpretation risks as well. Therefore, the methods of variant classification and accessible variant databases are mentioned. A useful strategy of clinical genetic testing with the application of both methodologies is presented. Finally, future directions and challenges are briefly commented on in this review.
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19
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Hare DJ, Vahey C, Walker S, Wittkowski A. Clinical psychologists' attitudes towards the biology and 'new genetics' of intellectual and developmental disabilities: a pilot study using Q-methodology. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2016; 60:1054-1065. [PMID: 26929020 DOI: 10.1111/jir.12261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 11/09/2015] [Accepted: 01/20/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The current study investigated how ideas and models from the 'New Genetics' and associated fields of developmental neuroscience and behavioural phenotypes are perceived by clinical psychologists working with people with intellectual and developmental disabilities (IDD). As well as examining the take-up and influence of such ideas, it also examines barriers, both personal and institutional, to the widespread adoption of such concepts and research findings in services for people with IDD. METHODS A Q-methodology study was undertaken with 31 qualified and 16 trainee clinical psychologists in the North West of England using a specifically developed 81-item Q set. RESULTS Three factors were identified and labelled Integration of social and medical models, Social model of disability is more helpful and Genetic advances in conflict with recognising the value of people with IDD. CONCLUSION There was a lack of consensus in clinical psychologists working with people with IDD, with amount and type of professional experience affecting the factor loadings, which may need to be considered in developing clinical applications of genetic IDD research.
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Affiliation(s)
- D J Hare
- School of Psychology, Cardiff University, Cardiff, Wales, UK.
| | | | - S Walker
- Socrates Clinical Psychology, Huddersfield, UK
| | - A Wittkowski
- School of Psychological Sciences, University of Manchester, Manchester, UK
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20
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Abstract
Stroke is the third leading cause of death worldwide after heart disease and all forms of cancers. Monogenic disorders, genetic, and environmental risk factors contribute to damaging cerebral blood vessels and, consequently, cause stroke. Developments in genomic research led to the discovery of numerous copy number variants (CNVs) that have been recently identified as a new tool for understanding the genetic basis of many diseases. This review discusses the current understanding of the types of stroke, the existing knowledge on the involvement of specific CNVs in stroke as well as the limitations of the methods used for detecting CNVs like SNP-microarray. To confirm an unequivocally association between CNVs and stroke and extend the current findings, it would be desirable to use another methodology to detect smaller CNVs or CNVs in genomic regions poorly covered by this technique, for instance, CGH-array.
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21
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Fontana P, Tortora C, Petillo R, Falco M, Miniero M, De Brasi D, Pisanti MA. A novel 5q11.2 microdeletion in a child with mild developmental delay and dysmorphic features. Am J Med Genet A 2016; 170:2445-8. [DOI: 10.1002/ajmg.a.37824] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 06/06/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Paolo Fontana
- Department of Molecular Medicine and Medical Biotechnologies; Federico II University of Naples; Naples Italy
| | - Cristina Tortora
- Department of Molecular Medicine and Medical Biotechnologies; Federico II University of Naples; Naples Italy
| | - Roberta Petillo
- Department of Experimental Medicine; Cardiomiology and Medical Genetics; Second University of Naples; Naples Italy
| | - Mariateresa Falco
- Department of Molecular Medicine and Medical Biotechnologies; Federico II University of Naples; Naples Italy
| | - Martina Miniero
- Department of Molecular Medicine and Medical Biotechnologies; Federico II University of Naples; Naples Italy
| | - Davide De Brasi
- Service of Medical Genetics; Cardarelli Hospital; Naples Italy
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Bengoa-Alonso A, Artigas-López M, Moreno-Igoa M, Cattalli C, Hernández-Charro B, Ramos-Arroyo MA. Delineation of a recognizable phenotype for the recurrent LCR22-C to D/E atypical 22q11.2 deletion. Am J Med Genet A 2016; 170:1485-94. [PMID: 26991864 DOI: 10.1002/ajmg.a.37614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 02/19/2016] [Indexed: 01/10/2023]
Abstract
The 22q11.2 deletion syndrome is typically caused by haploinsufficiency of a 3 Mb region that extends from LCR22-A until LCR22-D, while the recurrent recombination between any of the LCR22-D to H causes the 22q11.2 distal deletion syndrome. Here, we describe three patients with a de novo atypical ∼1.4 Mb 22q11.2 deletion that involves LCR22-C to a region beyond D (LCR22-C to D/E), encompassing the distal portion of the typical deleted region and the proximal portion of the distal deletion. We also review six previous published patients with the same rearrangement and compare their features with those found in patients with overlapping deletions. Patients with LCR22-C to D/E deletion present a recognizable phenotype characterized by facial dysmorphic features, high frequency of cardiac defects, including conotruncal defects, prematurity, growth restriction, microcephaly, and mild developmental delay. Genotype-phenotype analysis of the patients indicates that CRKL and MAPK1 genes play an important role as causative factors for the main clinical features of the syndrome. In particular, CRKL gene seems to be involved in the occurrence of conotruncal cardiac anomalies, mainly tetralogy of Fallot. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Amaya Bengoa-Alonso
- Department of Medical Genetics, Complejo Hospitalario de Navarra, IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Mercè Artigas-López
- Department of Medical Genetics, Complejo Hospitalario de Navarra, IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - María Moreno-Igoa
- Department of Medical Genetics, Complejo Hospitalario de Navarra, IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Claudio Cattalli
- Department of Medical Genetics, Complejo Hospitalario de Navarra, IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Blanca Hernández-Charro
- Department of Medical Genetics, Complejo Hospitalario de Navarra, IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Maria Antonia Ramos-Arroyo
- Department of Medical Genetics, Complejo Hospitalario de Navarra, IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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Carreira IM, Ferreira SI, Matoso E, Pires LM, Ferrão J, Jardim A, Mascarenhas A, Pinto M, Lavoura N, Pais C, Paiva P, Simões L, Caramelo F, Ramos L, Venâncio M, Ramos F, Beleza A, Sá J, Saraiva J, de Melo JB. Copy number variants prioritization after array-CGH analysis - a cohort of 1000 patients. Mol Cytogenet 2015; 8:103. [PMID: 26719768 PMCID: PMC4696247 DOI: 10.1186/s13039-015-0202-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/17/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Array-based comparative genomic hybridization has been assumed to be the first genetic test offered to detect genomic imbalances in patients with unexplained intellectual disability with or without dysmorphisms, multiple congenital anomalies, learning difficulties and autism spectrum disorders. Our study contributes to the genotype/phenotype correlation with the delineation of laboratory criteria which help to classify the different copy number variants (CNVs) detected. We clustered our findings into five classes ranging from an imbalance detected in a microdeletion/duplication syndrome region (class I) to imbalances that had previously been reported in normal subjects in the Database of Genomic Variants (DGV) and thus considered common variants (class IV). RESULTS All the analyzed 1000 patients had at least one CNV independently of its clinical significance. Most of them, as expected, were alterations already reported in the DGV for normal individuals (class IV) or without known coding genes (class III-B). In approximately 14 % of the patients an imbalance involving known coding genes, but with partially overlapping or low frequency of CNVs described in the DGV was identified (class IIIA). In 10.4 % of the patients a pathogenic CNV that explained the phenotype was identified consisting of: 40 class I imbalances, 44 class II de novo imbalances and 21 class II X-chromosome imbalances in male patients. In 20 % of the patients a familial pathogenic or potentially pathogenic CNV, consisting of inherited class II imbalances, was identified that implied a family evaluation by the clinical geneticists. CONCLUSIONS As this interpretation can be sometimes difficult, particularly if it is not possible to study the parents, using the proposed classification we were able to prioritize the multiple imbalances that are identified in each patient without immediately having to classify them as pathogenic or benign.
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Affiliation(s)
- Isabel Marques Carreira
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Susana Isabel Ferreira
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Eunice Matoso
- CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Laboratório de Citogenética, Hospital Pediátrico de Coimbra, Coimbra, Portugal
| | - Luís Miguel Pires
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - José Ferrão
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Ana Jardim
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Alexandra Mascarenhas
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Marta Pinto
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Nuno Lavoura
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Cláudia Pais
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Patrícia Paiva
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Lúcia Simões
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Francisco Caramelo
- Laboratório de Bioestatística e Informática Médica, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Lina Ramos
- Laboratório de Bioestatística e Informática Médica, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Margarida Venâncio
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Fabiana Ramos
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Ana Beleza
- Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joaquim Sá
- Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Jorge Saraiva
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joana Barbosa de Melo
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
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Lay-Son RG, León PL. [Current perspectives on genome-based diagnostic tests in Pediatrics]. REVISTA CHILENA DE PEDIATRIA 2015. [PMID: 26223391 DOI: 10.1016/j.rchipe.2015.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Etiological diagnosis is essential in the clinical management of individual patients. Some children with complex medical conditions are subjected to numerous testing, known as "diagnostic odyssey", which often gives no conclusive results. In recent years, a revolution in genomic medicine is underway with the use of technologies that promise to increase the ability to make a diagnosis and reduce the time involved. The main advantages and limitations of genomic diagnosis, as opposed to usual methodologies are reviewed with an emphasis on Pediatrics.
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Affiliation(s)
- R Guillermo Lay-Son
- Centro de Genética y Genómica, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, San Ramón, Santiago, Chile.
| | - P Luis León
- Centro de Genética y Genómica, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
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Sun G, Tan Z, Fan L, Wang J, Yang Y, Zhang W. 1q21.1 microduplication in a patient with mental impairment and congenital heart defect. Mol Med Rep 2015; 12:5655-8. [PMID: 26238956 PMCID: PMC4581767 DOI: 10.3892/mmr.2015.4166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 06/11/2015] [Indexed: 02/04/2023] Open
Abstract
1q21.1 duplication is a rare copy number variant with multiple congenital malformations, including developmental delay, autism spectrum disorder, dysmorphic features and congenital heart anomalies. The present study described a Chinese female patient (age, four years and eight months) with multiple malformations, including congenital heart defect, mental impairment and developmental delay. The parents and the monozygotic twin sister of the patient, however, were physically and psychologically normal. High-resolution genome-wide single nucleotide polymorphism array revealed a 1.6-Mb duplication in chromosome region 1q21.1. This chromosome region contained HFE2, a critical gene involved in hereditary hemochromatosis. However, the parents and monozygotic twin sister of the patient did not carry this genomic lesion. To the best of our knowledge, the present study was the first to report on a 1q21.1 duplication patient in mainland China.
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Affiliation(s)
- Guowen Sun
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zhiping Tan
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Liangliang Fan
- Clinical Center for Gene Diagnosis and Therapy of State Key Laboratory of Medical Genetics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Jian Wang
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Yifeng Yang
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Weizhi Zhang
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
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Abstract
The field of clinical genetics has advanced at an unprecedented pace. Today, with the aid of several high-resolution and high-precision technologies, physicians are able to make molecular genetic diagnoses for many infants affected with genetic disease. It is imperative, however, that perinatologists and neonatologists understand the strengths and limitations of genetic testing. This article discusses the different genetic testing options available for perinatal and neonatal diagnostics, along with their clinical utilities and indications. From variant-specific testing to whole-exome and genome sequencing, the article covers the whole gamut of genetic testing, with some thoughts on the changing paradigm of medical genetics.
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Affiliation(s)
- Arunkanth Ankala
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
| | - Madhuri R Hegde
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA.
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27
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Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies. JORNAL DE PEDIATRIA (VERSÃO EM PORTUGUÊS) 2015. [DOI: 10.1016/j.jpedp.2014.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Lay-Son G, Espinoza K, Vial C, Rivera JC, Guzmán ML, Repetto GM. Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies. J Pediatr (Rio J) 2015; 91:189-95. [PMID: 25458876 DOI: 10.1016/j.jped.2014.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/28/2014] [Accepted: 07/09/2014] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Clinical use of microarray-based techniques for the analysis of many developmental disorders has emerged during the last decade. Thus, chromosomal microarray has been positioned as a first-tier test. This study reports the first experience in a Chilean cohort. METHODS Chilean patients with developmental disabilities and congenital anomalies were studied with a high-density microarray (CytoScan™ HD Array, Affymetrix, Inc., Santa Clara, CA, USA). Patients had previous cytogenetic studies with either a normal result or a poorly characterized anomaly. RESULTS This study tested 40 patients selected by two or more criteria, including: major congenital anomalies, facial dysmorphism, developmental delay, and intellectual disability. Copy number variants (CNVs) were found in 72.5% of patients, while a pathogenic CNV was found in 25% of patients and a CNV of uncertain clinical significance was found in 2.5% of patients. CONCLUSION Chromosomal microarray analysis is a useful and powerful tool for diagnosis of developmental diseases, by allowing accurate diagnosis, improving the diagnosis rate, and discovering new etiologies. The higher cost is a limitation for widespread use in this setting.
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Affiliation(s)
- Guillermo Lay-Son
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, Santiago, Chile.
| | - Karena Espinoza
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Juan C Rivera
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - María L Guzmán
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, Santiago, Chile
| | - Gabriela M Repetto
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, Santiago, Chile
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Abstract
Schizophrenia is a common mental disorder, affecting 0.5-1% of the population. The mode of inheritance is complex and non-Mendelian with a high heritability of ca. 65-80%. Given this complexity, until most recently it was difficult to identify disease genes. But fortunately this has changed. Due to new technologies the last few years have brought highest interest in human genetics of complex diseases. The knowledge resulting from the availability of the complete sequence of the human genome, the systematic identification of single nucleotide polymorphisms (SNPs) throughout the genome, and the development of parallel genotyping technology (microarrays) established the conditions that brought about the current successful time in our ability to probe the genome for identifying disease genes. All these studies showed up new avenues for the biology of common complex diseases and yielded a multitude of genes showing strong association with complex diseases.
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31
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Snijders Blok C, Corsten-Janssen N, FitzPatrick DR, Romano C, Fichera M, Vitello GA, Willemsen MH, Schoots J, Pfundt R, van Ravenswaaij-Arts CM, Hoefsloot L, Kleefstra T. Definition of 5q11.2 microdeletion syndrome reveals overlap with CHARGE syndrome and 22q11 deletion syndrome phenotypes. Am J Med Genet A 2014; 164A:2843-8. [DOI: 10.1002/ajmg.a.36680] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/12/2014] [Indexed: 11/10/2022]
Affiliation(s)
| | - Nicole Corsten-Janssen
- Department of Genetics; University of Groningen, University Medical Center Groningen; Groningen The Netherlands
| | - David R. FitzPatrick
- MRC Human Genetics Unit, MRC IGMM; University of Edinburgh; Edinburgh United Kingdom
| | - Corrado Romano
- I.R.C.C.S. Associazione Oasi Maria Santissima; Troina Italy
| | - Marco Fichera
- I.R.C.C.S. Associazione Oasi Maria Santissima; Troina Italy
- Medical Genetics; University of Catania; Catania Italy
| | | | - Marjolein H. Willemsen
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Jeroen Schoots
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Lies Hoefsloot
- Clinical Genetics, Erasmus MC; University Medical Center Rotterdam; Rotterdam The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
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Gao X, Gotway G, Rathjen K, Johnston C, Sparagana S, Wise CA. Genomic Analyses of Patients With Unexplained Early-Onset Scoliosis. Spine Deform 2014; 2:324-332. [PMID: 27927329 PMCID: PMC4228381 DOI: 10.1016/j.jspd.2014.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 03/17/2014] [Accepted: 04/21/2014] [Indexed: 12/20/2022]
Abstract
STUDY DESIGN To test for rare genetic mutations, a cohort of patients with unexplained early-onset scoliosis (EOS) was screened using high-density microarray genotyping. A cohort of patients with adolescent idiopathic scoliosis (AIS) was similarly screened and the results were compared. SUMMARY OF BACKGROUND DATA Patients with scoliosis in infancy or early childhood (EOS) are at high risk for progressive deformity and associated problems including respiratory compromise. Early-onset scoliosis is frequently associated with genetic disorders but many patients present with nonspecific clinical features and without an associated diagnosis. The authors hypothesized that EOS in these patients may be caused by rare genetic mutations detectable by next-generation genomic methods. METHODS The researchers identified 24 patients with unexplained EOS from pediatric orthopedic clinics. They genotyped them, along with 39 connecting family members, using the Illumina OmniExpress-12, version 1.0 beadchip. Resulting genotypes were analyzed for chromosomal changes, specifically copy number variation and absence of heterozygosity. They screened 482 adolescent idiopathic scoliosis (AIS) patients and 744 healthy controls, who were similarly genotyped with the same beadchip, for chromosomal changes identified in the EOS cohort. RESULTS Copy number variation and absence of heterozygosity analyses revealed a genetic diagnosis of chromosome 15q24 microdeletion syndrome in 1 patient and maternal uniparental disomy of chromosome 14 in a second one. Prior genetic testing and clinical evaluations had been negative in both cases. A large novel chromosome 10 deletion was likely causal in a third EOS patient. These mutations identified in the EOS patients were absent in AIS patients and controls, and thus were not associated with AIS or found in asymptomatic individuals. CONCLUSIONS These data underscore the usefulness of updated genetic evaluations including high-density microarray-based genotyping and other next-generation methods in patients with unexplained EOS, even when prior genetic studies were negative. These data also suggest the intriguing possibility that other mutations detectable by whole genome sequencing, as well as epigenetic effects, await discovery in the EOS population.
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Affiliation(s)
- Xiaochong Gao
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children. Dallas, TX
| | - Garrett Gotway
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Karl Rathjen
- Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Charles Johnston
- Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Steven Sparagana
- Department of Neurology, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Carol A. Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children. Dallas, TX,Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX,To whom correspondence should be directed. Telephone: 214-559-7861 Fax: 214-559-7872
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Oliveira MM, Meloni VA, Canonaco RS, Takeno SS, Bortolai A, de Mello CB, de Lima FT, Melaragno MI. Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome in an adolescent with complex chromosomal rearrangement and intellectual disability. Am J Med Genet A 2014; 164A:2685-8. [PMID: 25081192 DOI: 10.1002/ajmg.a.36690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/27/2014] [Indexed: 01/02/2023]
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Abstract
Chromosome 17q21.31 microdeletion syndrome is a genomic disorder caused by a recurrent 600 kb long deletion. The deletion affects the region of a common inversion present in about 20% of Europeans. The inversion is associated with the H2 haplotype carrying additional low-copy repeats susceptible to non-allelic homologous recombination, and this haplotype is prone to deletion. No instances of 17q21.31 deletions inherited from an affected parent have been reported, and the deletions always affected a parental chromosome with the H2 haplotype. The syndrome is characterized clinically by intellectual disability, hypotonia, friendly behavior and specific facial dysmorphism with long face, large tubular or pear-shaped nose and bulbous nasal tip. We present monozygotic twin sisters showing the typical clinical picture of the syndrome. The phenotype of the sisters was very similar, with a slightly more severe presentation in Twin B. The 17q21.31 microdeletion was confirmed in both patients but in neither of their parents. Potential copy number differences between the genomes of the twins were subsequently searched using high-resolution single nucleotide polymorphism (SNP) and comparative genome hybridisation (CGH) arrays. However, these analyses identified no additional aberrations or genomic differences that could potentially be responsible for the subtle phenotypic differences. These could possibly be related to the more severe perinatal history of Twin B, or to the variable expressivity of the disorder. In accord with the expectations, one of the parents (the mother) was shown to carry the H2 haplotype, and the maternal allele of chromosome 17q21.31 was missing in the twins.
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Masurel-Paulet A, Drumare I, Holder M, Cuisset JM, Vallée L, Defoort S, Bourgois B, Pernes P, Cuvellier JC, Huet F, Chehadeh SE, Thevenon J, Callier P, Thauvin C, Faivre L, Andrieux J. Further delineation of eye manifestations in homozygous 15q13.3 microdeletions including TRPM1: a differential diagnosis of ceroid lipofuscinosis. Am J Med Genet A 2014; 164A:1537-44. [PMID: 24668847 DOI: 10.1002/ajmg.a.36471] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 12/31/2013] [Indexed: 11/11/2022]
Abstract
The 15q13.3 heterozygous microdeletion is a fairly common microdeletion syndrome with marked clinical variability and incomplete penetrance. The average size of the deletion, which comprises six genes including CHRNA7, is 1.5 Mb. CHRNA7 has been identified as the gene responsible for the neurological phenotype in this microdeletion syndrome. Only seven patients with a homozygous microdeletion that includes at least CHRNA7, and is inherited from both parents have been described in the literature. The aim of this study was to further describe the distinctive eye manifestations from the analysis in the three French patients diagnosed with the classical 1.5 Mb homozygous microdeletion. Patients' ages ranged from 30 months to 9 years, and included one sib pair. They all displayed a remarkably severe identifiable clinical phenotype that included congenital blindness and convulsive encephalopathy with inconstant abnormal movements. The ophthalmological examination revealed a lack of eye tracking, optic nerve pallor, an immature response with increased latencies with no response to the checkerboard stimulations at the visual evoked potential examination, and a distinctive retina dystrophy with a negative electroretinogram in which the "b" wave was smaller than the "a" wave after a dark adapted pupil and bright flash in all patients. Clear genotype-phenotype correlations emerged, showing that this eye phenotype was secondary to homozygous deletion of TRPM1, the gene responsible for autosomal recessive congenital stationary night blindness. The main differential diagnosis is ceroid lipofuscinosis.
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Affiliation(s)
- Alice Masurel-Paulet
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, CHU Dijon, France
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Fontana P, Genesio R, Casertano A, Cappuccio G, Mormile A, Nitsch L, Iolascon A, Andria G, Melis D. Loeys–Dietz syndrome type 4, caused by chromothripsis, involving the TGFB2 gene. Gene 2014; 538:69-73. [DOI: 10.1016/j.gene.2014.01.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/29/2013] [Accepted: 01/03/2014] [Indexed: 12/20/2022]
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37
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Giltay JC, Maiburg MC. Klinefelter syndrome: clinical and molecular aspects. Expert Rev Mol Diagn 2014; 10:765-76. [DOI: 10.1586/erm.10.63] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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38
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Detection of chromosomal imbalances using combined MLPA kits in patients with syndromic intellectual disability. REV ROMANA MED LAB 2014. [DOI: 10.2478/rrlm-2014-0019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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39
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Bartnik M, Nowakowska B, Derwińska K, Wiśniowiecka-Kowalnik B, Kędzior M, Bernaciak J, Ziemkiewicz K, Gambin T, Sykulski M, Bezniakow N, Korniszewski L, Kutkowska-Kaźmierczak A, Klapecki J, Szczałuba K, Shaw CA, Mazurczak T, Gambin A, Obersztyn E, Bocian E, Stankiewicz P. Application of array comparative genomic hybridization in 256 patients with developmental delay or intellectual disability. J Appl Genet 2013; 55:125-44. [PMID: 24297458 PMCID: PMC3909616 DOI: 10.1007/s13353-013-0181-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/17/2013] [Accepted: 10/20/2013] [Indexed: 12/22/2022]
Abstract
We used whole-genome exon-targeted oligonucleotide array comparative genomic hybridization (array CGH) in a cohort of 256 patients with developmental delay (DD)/intellectual disability (ID) with or without dysmorphic features, additional neurodevelopmental abnormalities, and/or congenital malformations. In 69 patients, we identified 84 non-polymorphic copy-number variants, among which 41 are known to be clinically relevant, including two recently described deletions, 4q21.21q21.22 and 17q24.2. Chromosomal microarray analysis revealed also 15 potentially pathogenic changes, including three rare deletions, 5q35.3, 10q21.3, and 13q12.11. Additionally, we found 28 copy-number variants of unknown clinical significance. Our results further support the notion that copy-number variants significantly contribute to the genetic etiology of DD/ID and emphasize the efficacy of the detection of novel candidate genes for neurodevelopmental disorders by whole-genome array CGH.
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Affiliation(s)
- Magdalena Bartnik
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
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40
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The advantage of using SNP array in clinical testing for hematological malignancies—a comparative study of three genetic testing methods. Cancer Genet 2013; 206:317-26. [DOI: 10.1016/j.cancergen.2013.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 11/18/2022]
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41
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Willemsen M, Kleefstra T. Making headway with genetic diagnostics of intellectual disabilities. Clin Genet 2013; 85:101-10. [DOI: 10.1111/cge.12244] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/24/2013] [Accepted: 07/24/2013] [Indexed: 01/31/2023]
Affiliation(s)
- M.H. Willemsen
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
| | - T. Kleefstra
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
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42
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Eto K, Sakai N, Shimada S, Shioda M, Ishigaki K, Hamada Y, Shinpo M, Azuma J, Tominaga K, Shimojima K, Ozono K, Osawa M, Yamamoto T. Microdeletions of 3p21.31 characterized by developmental delay, distinctive features, elevated serum creatine kinase levels, and white matter involvement. Am J Med Genet A 2013; 161A:3049-56. [DOI: 10.1002/ajmg.a.36156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 06/27/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Kaoru Eto
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
| | - Norio Sakai
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Shino Shimada
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
| | - Mutsuki Shioda
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
| | - Keiko Ishigaki
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
| | - Yusuke Hamada
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Michiko Shinpo
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Junji Azuma
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Koji Tominaga
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Keiko Shimojima
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
| | - Keiichi Ozono
- Department of Pediatrics; Osaka University Graduate School of Medicine; Suita Japan
| | - Makiko Osawa
- Department of Pediatrics; Tokyo Women's Medical University; Tokyo Japan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
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Tzagkaraki E, Sofocleous C, Fryssira-Kanioura H, Dinopoulos A, Goulielmos G, Mavrou A, Kitsiou-Tzeli S, Kanavakis E, Sofia KT, Kanavakis E. Screening of UBE3A gene in patients referred for Angelman Syndrome. Eur J Paediatr Neurol 2013; 17:366-73. [PMID: 23416059 DOI: 10.1016/j.ejpn.2012.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 12/27/2012] [Accepted: 12/30/2012] [Indexed: 01/05/2023]
Abstract
Angelman Syndrome (AS) is a neurodevelopmental disorder characterized by severe developmental delay, speech impairment and unique behaviors including inappropriate laughter and happy disposition. AS is related to deficient maternal UBE3A gene expression caused either by chromosomal deletions, uniparental disomy, molecular defects of the imprinted 15q11-q13 critical region or by loss of function mutations in the maternally inherited UBE3A. In the present study, screening UBE3A was performed in 43 patients who were referred for AS but whom previous molecular diagnostic tests failed to provide a diagnosis. Two causative mutations--one of them novel--and four polymorphic variants one of which is also novel were revealed. Further investigation of 7 patients disclosed defects in other genes involved in clinical phenotypes mimicking AS. A typical EEG pattern and microcephaly in patients with developmental delay prompt for AS investigation while wide genetic screening should be applied to help resolution of the complex phenotypes characterized by developmental delay.
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Affiliation(s)
- Evmorfia Tzagkaraki
- Department of Medical Genetics, University of Athens School of Medicine, Choremeio Research Laboratory, Aghia Sophia Children's Hospital, Thivon and Levadeias str, 11527 Goudi, Athens, Greece.
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Acharya K. Prenatal testing for intellectual disability: misperceptions and reality with lessons from Down syndrome. ACTA ACUST UNITED AC 2013; 17:27-31. [PMID: 22447752 DOI: 10.1002/ddrr.135] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Down syndrome is the most common cause of intellectual disability. In the United States, it is recommended that prenatal testing for Down syndrome be offered to all women. Because of this policy and consequent public perception, having Down syndrome has become a disadvantage in the prenatal period. However, in the postnatal period, there may be some advantage in having Down syndrome. To help parents make informed decisions about screening and testing, it is crucial to reconcile divergent prenatal and postnatal perspectives. Advancements in genetic technologies will also impact the informed consent process and need to be considered.
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Affiliation(s)
- Kruti Acharya
- Departments of Medicine and Pediatrics, MacLean Center for Clinical Medical Ethics, University of Chicago, Chicago, Illinois, USA.
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45
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Ganesamoorthy D, Bruno DL, McGillivray G, Norris F, White SM, Adroub S, Amor DJ, Yeung A, Oertel R, Pertile MD, Ngo C, Arvaj AR, Walker S, Charan P, Palma-Dias R, Woodrow N, Slater HR. Meeting the challenge of interpreting high-resolution single nucleotide polymorphism array data in prenatal diagnosis: does increased diagnostic power outweigh the dilemma of rare variants? BJOG 2013; 120:594-606. [PMID: 23332022 DOI: 10.1111/1471-0528.12150] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2012] [Indexed: 01/14/2023]
Abstract
OBJECTIVE Several studies have already shown the superiority of chromosomal microarray analysis (CMA) compared with conventional karyotyping for prenatal investigation of fetal ultrasound abnormality. This study used very high-resolution single nucleotide polymorphism (SNP) arrays to determine the impact on detection rates of all clinical categories of copy number variations (CNVs), and address the issue of interpreting and communicating findings of uncertain or unknown clinical significance, which are to be expected at higher frequency when using very high-resolution CMA. DESIGN Prospective validation study. SETTING Tertiary clinical genetics centre. POPULATION Women referred for further investigation of fetal ultrasound anomaly. METHODS We prospectively tested 104 prenatal samples using both conventional karyotyping and high-resolution arrays. MAIN OUTCOME MEASURES The detection rates for each clinical category of CNV. RESULTS Unequivocal pathogenic CNVs were found in six cases, including one with uniparental disomy (paternal UPD 14). A further four cases had a 'likely pathogenic' finding. Overall, CMA improved the detection of 'pathogenic' and 'likely pathogenic' abnormalities from 2.9% (3/104) to 9.6% (10/104). CNVs of 'unknown' clinical significance that presented interpretational difficulties beyond results from parental investigations were detected in 6.7% (7/104) of samples. CONCLUSIONS Increased detection sensitivity appears to be the main benefit of high-resolution CMA. Despite this, in this cohort there was no significant benefit in terms of improving detection of small pathogenic CNVs. A potential disadvantage is the high detection rate of CNVs of 'unknown' clinical significance. These findings emphasise the importance of establishing an evidence-based policy for the interpretation and reporting of CNVs, and the need to provide appropriate pre- and post-test counselling.
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Affiliation(s)
- D Ganesamoorthy
- VCGS Cytogenetics Laboratory, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
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Florisson JMG, Mathijssen IMJ, Dumee B, Hoogeboom JAM, Poddighe PJ, Oostra BA, Frijns JP, Koster L, de Klein A, Eussen B, de Vries BBA, Swagemakers S, van der Spek PJ, Verkerk AJMH. Complex craniosynostosis is associated with the 2p15p16.1 microdeletion syndrome. Am J Med Genet A 2013; 161A:244-53. [PMID: 23303641 DOI: 10.1002/ajmg.a.35632] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 07/28/2012] [Indexed: 12/29/2022]
Abstract
In a screening project of patients with (complex) craniosynostosis using genomic arrays, we identified two patients with craniosynostosis and microcephaly with a deletion in the 2p15p16.1 chromosomal region. This region has been associated with a new microdeletion syndrome, for which patients have various features in common, including microcephaly and intellectual disability. Deletions were identified using Affymetrix 250K SNP array and further characterized by fluorescence in situ hybridization (FISH) analysis and qPCR. The deletions in our two patients overlapped within the 2p15p16.1 microdeletion syndrome area and were 6.8 and 6.9 Mb in size, respectively. FISH and qPCR confirmed the presence of only one copy in this region. Finemapping of the breakpoints indicated precise borders in our patients and were further finemapped in two other previously reported patients. Clinical features of patients with deletions in the 2p15p16.1 region vary. Including data from our patients, now eight out of nine reported patients have microcephaly, one of the major features, and all had intellectual disability. The current reported two patients add different forms of craniosynostosis to the clinical spectrum of this recently recognized microdeletion syndrome.
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Affiliation(s)
- Joyce M G Florisson
- Department of Plastic and Reconstructive Surgery, Erasmus University Medical Centre, Rotterdam, The Netherlands
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Abstract
Epilepsy is a feature of several hundred chromosome abnormalities. However, there are relatively few conditions in which epilepsy is a consistent feature and even fewer in which the electroclinical phenotype is recognizable. Advances in cytogenetics and molecular genetics are leading to the detection of more complex and smaller chromosomal re-arrangements, duplications, and deletions using techniques such as comparative genome hybridization (CGH). This will provide new challenges for the epilepsy specialist who, in partnership with the geneticist, will have to judge the clinical relevance of these abnormalities. Most chromosome anomalies associated with epilepsy are individually rare therefore clinicians must continue to collaborate to describe novel electroclinical phenotypes. Cytogenetic studies should be requested in all individuals with refractory epilepsy and no clear underlying cause even in cases with no dysmorphic features, no learning disability, and an EEG suggestive of genetic generalized epilepsy. In syndromes where epilepsy is a consistent feature the seizure semiology and EEG features can suggest a specific diagnosis and guide the clinician to the appropriate cytogenetic investigation. An early correct diagnosis can save unnecessary investigations and guide prognosis. Children with chromosomal disorders frequently have learning disability, which can be further compromised by an epileptic encephalopathy. Medications should be targeted to specific seizure types.
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Affiliation(s)
- Sameer M Zuberi
- Fraser of Allander Neurosciences Unit, Royal Hospital for Sick Children, Glasgow, UK.
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48
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Cacabelos R, Cacabelos P, Aliev G. Genomics of schizophrenia and pharmacogenomics of antipsychotic drugs. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ojpsych.2013.31008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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49
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Iourov IY, Vorsanova SG, Kurinnaia OS, Zelenova MA, Silvanovich AP, Yurov YB. Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies. Mol Cytogenet 2012; 5:46. [PMID: 23272938 PMCID: PMC3547809 DOI: 10.1186/1755-8166-5-46] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 12/14/2012] [Indexed: 01/28/2023] Open
Abstract
Background Array comparative genomic hybridization (CGH) has been repeatedly shown to be a successful tool for the identification of genomic variations in a clinical population. During the last decade, the implementation of array CGH has resulted in the identification of new causative submicroscopic chromosome imbalances and copy number variations (CNVs) in neuropsychiatric (neurobehavioral) diseases. Currently, array-CGH-based technologies have become an integral part of molecular diagnosis and research in individuals with neuropsychiatric disorders and children with intellectual disability (mental retardation) and congenital anomalies. Here, we introduce the Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies analyzed by BAC array CGH and a novel bioinformatic strategy. Results Among 54 individuals highly selected according to clinical criteria and molecular and cytogenetic data (from 2426 patients evaluated cytogenetically and molecularly between November 2007 and May 2012), chromosomal imbalances were detected in 26 individuals (48%). In two patients (4%), a previously undescribed condition was observed. The latter has been designated as meiotic (constitutional) genomic instability resulted in multiple submicroscopic rearrangements (including CNVs). Using bioinformatic strategy, we were able to identify clinically relevant CNVs in 15 individuals (28%). Selected cases were confirmed by molecular cytogenetic and molecular genetic methods. Eight out of 26 chromosomal imbalances (31%) have not been previously reported. Among them, three cases were co-occurrence of subtle chromosome 9 and 21 deletions. Conclusions We conducted an array CGH study of Russian patients suffering from intellectual disability, autism, epilepsy and congenital anomalies. In total, phenotypic manifestations of clinically relevant genomic variations were found to result from genomic rearrangements affecting 1247 disease-causing and pathway-involved genes. Obviously, a significantly lesser part of them are true candidates for intellectual disability, autism or epilepsy. The success of our preliminary array CGH and bioinformatic study allows us to expand the cohort. According to the available literature, this is the first comprehensive array CGH evaluation of a Russian cohort of children with neuropsychiatric disorders and congenital anomalies.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, Russian Academy of Medical Sciences, 119152, Moscow, Russia.
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50
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Egger JI, Wingbermühle E, Verhoeven WM, Dijkman M, Radke S, de Bruijn ER, de Vries B, Kessels RP, Koolen D. Hypersociability in the behavioral phenotype of 17q21.31 microdeletion syndrome. Am J Med Genet A 2012; 161A:21-6. [DOI: 10.1002/ajmg.a.35652] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/13/2012] [Indexed: 11/12/2022]
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