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Paparella A, L’Abbate A, Palmisano D, Chirico G, Porubsky D, Catacchio CR, Ventura M, Eichler EE, Maggiolini FAM, Antonacci F. Structural Variation Evolution at the 15q11-q13 Disease-Associated Locus. Int J Mol Sci 2023; 24:15818. [PMID: 37958807 PMCID: PMC10648317 DOI: 10.3390/ijms242115818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The impact of segmental duplications on human evolution and disease is only just starting to unfold, thanks to advancements in sequencing technologies that allow for their discovery and precise genotyping. The 15q11-q13 locus is a hotspot of recurrent copy number variation associated with Prader-Willi/Angelman syndromes, developmental delay, autism, and epilepsy and is mediated by complex segmental duplications, many of which arose recently during evolution. To gain insight into the instability of this region, we characterized its architecture in human and nonhuman primates, reconstructing the evolutionary history of five different inversions that rearranged the region in different species primarily by accumulation of segmental duplications. Comparative analysis of human and nonhuman primate duplication structures suggests a human-specific gain of directly oriented duplications in the regions flanking the GOLGA cores and HERC segmental duplications, representing potential genomic drivers for the human-specific expansions. The increasing complexity of segmental duplication organization over the course of evolution underlies its association with human susceptibility to recurrent disease-associated rearrangements.
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Affiliation(s)
- Annalisa Paparella
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Alberto L’Abbate
- Institute of Biomembranes, Bioenergetics, and Molecular Biotechnology (IBIOM), 70125 Bari, Italy
| | - Donato Palmisano
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Gerardina Chirico
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Claudia R. Catacchio
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Mario Ventura
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute (HHMI), University of Washington, Seattle, WA 98195, USA
| | - Flavia A. M. Maggiolini
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA), 70010 Bari, Italy
| | - Francesca Antonacci
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
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Song J, Liu X, Zhang C, Xu F, Wang B. Clinical and genetic study of three families with 15q11q13 duplications. Taiwan J Obstet Gynecol 2022; 61:717-721. [PMID: 35779929 DOI: 10.1016/j.tjog.2021.12.004] [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] [Accepted: 12/02/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To report three families with chromosome 15q11q13 duplications. CASE REPORT We report the prenatal diagnosis and genetic counseling of three 15q11q13 duplications. CONCLUSION Chromosomal microdeletions and microduplications are difficult to be detected by conventional cytogenetics. With molecular genetic techniques including array-based methods, the number of reported cases has rapidly increased. An integration of prenatal ultrasound, NIPT, karyotype analysis, CMA and genetic counseling is helpful for the prenatal diagnosis of chromosomal microdeletions/microduplications.
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Affiliation(s)
- Jieping Song
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Xu Liu
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Chengcheng Zhang
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Fei Xu
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bo Wang
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China.
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Nicolle R, Siquier-Pernet K, Rio M, Guimier A, Ollivier E, Nitschke P, Bole-Feysot C, Romana S, Hastie A, Cantagrel V, Malan V. 16p13.11p11.2 triplication syndrome: a new recognizable genomic disorder characterized by optical genome mapping and whole genome sequencing. Eur J Hum Genet 2022; 30:712-720. [PMID: 35388186 PMCID: PMC9177583 DOI: 10.1038/s41431-022-01094-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 03/06/2022] [Accepted: 03/21/2022] [Indexed: 11/09/2022] Open
Abstract
Highly identical segmental duplications (SDs) account for over 5% of the human genome and are enriched in the short arm of the chromosome 16. These SDs are susceptibility factors for recurrent chromosomal rearrangements mediated by non-allelic homologous recombination (NAHR). Chromosomal microarray analysis (CMA) has been widely used as the first-tier test for individuals with developmental disabilities and/or congenital anomalies and several genomic disorders involving the 16p-arm have been identified with this technique. However, the resolution of CMA and the limitations of short-reads whole genome sequencing (WGS) technology do not allow the full characterization of the most complex chromosomal rearrangements. Herein, we report on two unrelated patients with a de novo 16p13.11p11.2 triplication associated with a 16p11.2 duplication, detected by CMA. These patients share a similar phenotype including hypotonia, severe neurodevelopmental delay with profound speech impairment, hyperkinetic behavior, conductive hearing loss, and distinctive facial features. Short-reads WGS could not map precisely any of the rearrangement's breakpoints that lie within SDs. We used optical genome mapping (OGM) to determine the relative orientation of the triplicated and duplicated segments as well as the genomic positions of the breakpoints, allowing us to propose a mechanism involving recombination between allelic SDs and a NAHR event. In conclusion, we report a new clinically recognizable genomic disorder. In addition, the mechanism of these complex chromosomal rearrangements involving SDs could be unraveled by OGM.
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Affiliation(s)
- Romain Nicolle
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Karine Siquier-Pernet
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Marlène Rio
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Anne Guimier
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
| | - Emmanuelle Ollivier
- Université de Paris, Bioinformatics Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Patrick Nitschke
- Université de Paris, Bioinformatics Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Christine Bole-Feysot
- Université de Paris, Genomics Platform, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Serge Romana
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | | | - Vincent Cantagrel
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Valérie Malan
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France.
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France.
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Chilakamarri L, Mellin‐Sanchez EL. Complex chromosomal rearrangement involving 15q11‐q13 interstitial triplication and duplication: A new case report of dysmorphic and neuropsychiatric features. Clin Case Rep 2022; 10:e05835. [PMID: 35600042 PMCID: PMC9107916 DOI: 10.1002/ccr3.5835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Lekha Chilakamarri
- University of Texas Rio Grande Valley School of Medicine Edinburg Texas USA
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Cirillo E, Prencipe MR, Giardino G, Romano R, Scalia G, Genesio R, Nitsch L, Pignata C. Clinical Phenotype, Immunological Abnormalities, and Genomic Findings in Patients with DiGeorge Spectrum Phenotype without 22q11.2 Deletion. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2020; 8:3112-3120. [DOI: 10.1016/j.jaip.2020.06.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023]
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Yanagishita T, Imaizumi T, Yamamoto-Shimojima K, Yano T, Okamoto N, Nagata S, Yamamoto T. Breakpoint junction analysis for complex genomic rearrangements with the caldera volcano-like pattern. Hum Mutat 2020; 41:2119-2127. [PMID: 32906213 DOI: 10.1002/humu.24108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/25/2020] [Accepted: 09/06/2020] [Indexed: 12/16/2022]
Abstract
Chromosomal triplications can be classified into recurrent and nonrecurrent triplications. Most of the nonrecurrent triplications are embedded in duplicated segments, and duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) has been established as one of the mechanisms of triplication. This study aimed to reveal the underlying mechanism of the TRP-DUP-TRP pattern of chromosomal aberrations, in which the appearance of moving averages obtained through array-based comparative genomic hybridization analysis is similar to the shadows of the caldera volcano-like pattern, which were first identified in two patients with neurodevelopmental disabilities. For this purpose, whole-genome sequencing using long-read Nanopore sequencing was carried out to confirm breakpoint junctions. Custom array analysis and Sanger sequencing were also used to detect all breakpoint junctions. As a result, the TRP-DUP-TRP pattern consisted of only two patterns of breakpoint junctions in both patients. In patient 1, microhomologies were identified in breakpoint junctions. In patient 2, more complex architectures with insertional segments were identified. Thus, replication-based mechanisms were considered as a mechanism of the TRP-DUP-TRP pattern.
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Affiliation(s)
- Tomoe Yanagishita
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.,Department of Genomic Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Taichi Imaizumi
- Department of Genomic Medicine, Tokyo Women's Medical University, Tokyo, Japan.,Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | | | - Tamami Yano
- Department of Pediatrics, Akita University, Akita, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Satoru Nagata
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.,Department of Genomic Medicine, Tokyo Women's Medical University, Tokyo, Japan.,Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan.,Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
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Lu Y, Liang Y, Ning S, Deng G, Xie Y, Song J, Zuo N, Feng C, Qin Y. Rare partial trisomy and tetrasomy of 15q11-q13 associated with developmental delay and autism spectrum disorder. Mol Cytogenet 2020; 13:21. [PMID: 32536972 PMCID: PMC7288499 DOI: 10.1186/s13039-020-00489-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/26/2020] [Indexed: 11/24/2022] Open
Abstract
Background Small supernumerary marker chromosomes (sSMCs), are additional abnormal chromosomes, which can’t be detected accurately by banding cytogenetic analysis. Abnormal phenotypes were observed in about 30% of SMC carriers. Duplication of chromosome 15 and related disorders, characterized by hypotonia motor delays, autism spectrum disorder (ASD), intellectual disability, and epilepsy including infantile spasms, might be account for 50% of the total sSMCs. Case presentation An 11-month-old infant with an sSMC found by banding cytogenetics was referred to our clinic because of developmental retardation and autism spectrum disorder. After several months of rehabilitation treatment, the progress of motor development was obvious, but the consciousness was still far from satisfied. High-resolution karyotype analysis, multiplex ligation-dependent probe amplification and copy number variation sequencing (CNV-Seq) were conducted to confirm the identity of the sSMC. A bisatellited dicentric sSMC was observed clearly in high-resolution karyotype analysis and a 10.16-Mb duplication of 15q11.1q13.2 (3.96 copies) together with a 1.84-Mb duplication of 15q13.2q13.3 (3 copies) was showed by CNV-Seq in the proband. It suggested that the molecular cytogenetic karyotype was 47,XY,+dic(15;15)(q13.2;q13.3). Furthermore, the clinical symptoms of the proband mostly fit 15q duplication related disorders which are characterized by hypotonia motor delays, autism spectrum disorder (ASD), and intellectual disability. Conclusion We reported for the first time using CNV-Seq to detect sSMCs and find a partial trisomy and tetrasomy of 15q11-q13 associated with developmental delay and autism spectrum disorder. Our report indicates that CNV-seq is a useful and economical way for diagnosis of dup15q and related disorders.
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Affiliation(s)
- Yinghong Lu
- Department of Clinical Laboratory, Yulin Women and Children Care Hospital, Yulin, Guangxi Zhuang Autonomous Region 537000 People's Republic of China
| | - Yi Liang
- Department of Clinical Laboratory, Yulin Women and Children Care Hospital, Yulin, Guangxi Zhuang Autonomous Region 537000 People's Republic of China
| | - Sisi Ning
- Department of Clinical Laboratory, Yulin Women and Children Care Hospital, Yulin, Guangxi Zhuang Autonomous Region 537000 People's Republic of China
| | - Guosheng Deng
- Department of Clinical Laboratory, Yulin Women and Children Care Hospital, Yulin, Guangxi Zhuang Autonomous Region 537000 People's Republic of China
| | - Yuling Xie
- Department of Clinical Laboratory, Yulin Women and Children Care Hospital, Yulin, Guangxi Zhuang Autonomous Region 537000 People's Republic of China
| | - Jujie Song
- Department of Clinical Laboratory, Yulin Women and Children Care Hospital, Yulin, Guangxi Zhuang Autonomous Region 537000 People's Republic of China
| | - Na Zuo
- Department of Clinical Laboratory, Yulin Women and Children Care Hospital, Yulin, Guangxi Zhuang Autonomous Region 537000 People's Republic of China
| | - Chunfeng Feng
- Department of Clinical Laboratory, Yulin Women and Children Care Hospital, Yulin, Guangxi Zhuang Autonomous Region 537000 People's Republic of China
| | - Yunrong Qin
- Department of Clinical Laboratory, Yulin Women and Children Care Hospital, Yulin, Guangxi Zhuang Autonomous Region 537000 People's Republic of China
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Li X, Shi G, Li Y, Zhang X, Xiang Y, Wang T, Li Y, Chen H, Fu Q, Zhang H, Wang B. 15q11.2 deletion is enriched in patients with total anomalous pulmonary venous connection. J Med Genet 2020; 58:jmedgenet-2019-106608. [PMID: 32376791 DOI: 10.1136/jmedgenet-2019-106608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 02/02/2023]
Abstract
INTRODUCTION CNV is a vital pathogenic factor of congenital heart disease (CHD). However, few CNVs have been reported for total anomalous pulmonary venous connection (TAPVC), which is a rare form of CHD. Using case-control study, we identified 15q11.2 deletion associated with TAPVC. We then used a TAPVC trio as model to reveal possible molecular basis of 15q11.2 microdeletion. METHODS CNVplex and Chromosomal Microarray were used to identify and validate CNVs in samples from 231 TAPVC cases and 200 healthy controls from Shanghai Children's Medical Center. In vitro cardiomyocyte differentiation of induced pluripotent stem cells from peripheral blood mononuclear cells for a TAPVC trio with paternal inherited 15q11.2 deletion was performed to characterise the effect of the deletion on cardiomyocyte differentiation and gene expression. RESULTS The 15q11.2 microdeletion was significantly enriched in patients with TAPVC compared with healthy control (13/231 in patients vs 0/200 in controls, p=5.872×10-2, Bonferroni adjusted) using Fisher's exact test. Induced pluripotent stem cells from the proband could not differentiate into normal cardiomyocyte. Transcriptomic analysis identified a number of differentially expressed genes in the 15q11.2 deletion carriers of the family. TAPVC disease-causing genes such as PITX2, NKX2-5 and ANKRD1 showed significantly higher expression in the proband compared with her healthy mother. Knockdown of TUBGCP5 could lead to abnormal cardiomyocyte differentiation. CONCLUSION We discovered that the 15q11.2 deletion is significantly associated with TAPVC. Gene expression profile that might arise from 15q11.2 deletion for a TAPVC family was characterised using cell experiments.
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Affiliation(s)
- Xiaoliang Li
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guocheng Shi
- Department of Cardiothoracic Surgery, Heart Center, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yang Li
- Department of Hematology & Oncology, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoqing Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ying Xiang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Teng Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yanxin Li
- Department of Hematology & Oncology, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huiwen Chen
- Department of Cardiothoracic Surgery, Heart Center, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hong Zhang
- Department of Obestetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Bo Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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Catusi I, Recalcati MP, Bestetti I, Garzo M, Valtorta C, Alfonsi M, Alghisi A, Cappellani S, Casalone R, Caselli R, Ceccarini C, Ceglia C, Ciaschini AM, Coviello D, Crosti F, D'Aprile A, Fabretto A, Genesio R, Giagnacovo M, Granata P, Longo I, Malacarne M, Marseglia G, Montaldi A, Nardone AM, Palka C, Pecile V, Pessina C, Postorivo D, Redaelli S, Renieri A, Rigon C, Tiberi F, Tonelli M, Villa N, Zilio A, Zuccarello D, Novelli A, Larizza L, Giardino D. Testing single/combined clinical categories on 5110 Italian patients with developmental phenotypes to improve array-based detection rate. Mol Genet Genomic Med 2019; 8:e1056. [PMID: 31851782 PMCID: PMC6978242 DOI: 10.1002/mgg3.1056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023] Open
Abstract
Background Chromosomal microarray analysis (CMA) is nowadays widely used in the diagnostic path of patients with clinical phenotypes. However, there is no ascertained evidence to date on how to assemble single/combined clinical categories of developmental phenotypic findings to improve the array‐based detection rate. Methods The Italian Society of Human Genetics coordinated a retrospective study which included CMA results of 5,110 Italian patients referred to 17 genetics laboratories for variable combined clinical phenotypes. Results Non‐polymorphic copy number variants (CNVs) were identified in 1512 patients (30%) and 615 (32%) present in 552 patients (11%) were classified as pathogenic. CNVs were analysed according to type, size, inheritance pattern, distribution among chromosomes, and association to known syndromes. In addition, the evaluation of the detection rate of clinical subgroups of patients allowed to associate dysmorphisms and/or congenital malformations combined with any other single clinical sign to an increased detection rate, whereas non‐syndromic neurodevelopmental signs and non‐syndromic congenital malformations to a decreased detection rate. Conclusions Our retrospective study resulted in confirming the high detection rate of CMA and indicated new clinical markers useful to optimize their inclusion in the diagnostic and rehabilitative path of patients with developmental phenotypes.
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Affiliation(s)
- Ilaria Catusi
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | | | - Ilaria Bestetti
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Maria Garzo
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Chiara Valtorta
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Melissa Alfonsi
- U.O.C. di Genetica medica, Ospedale SS Annunziata, Chieti, Italy
| | - Alberta Alghisi
- U.O.S. Genetica e Biologia Molecolare, Azienda ULSS 6, Vicenza, Italy
| | | | - Rosario Casalone
- SMeL specializzato Citogenetica e Genetica Medica, ASST Sette Laghi, Osp. di Circolo e Fond. Macchi, Varese, Italy
| | - Rossella Caselli
- U.O.C. Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Carlo Ceglia
- UOSD Genetica Medica, AORN "SG Moscati", Avellino, Italy
| | - Anna Maria Ciaschini
- A.O.U. Ospedali Riuniti Umberto I - G.M.Lancisi - G.Salesi, Lab. Genetica Medica SOS Malattie Rare, Ancona, Italy
| | - Domenico Coviello
- Lab. di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Francesca Crosti
- U.S. Genetica Medica, Ospedale San Gerardo ASST Monza, Monza, Italy
| | | | | | - Rita Genesio
- U.O.C. di Citogenetica, A.O.U. Federico II, Napoli, Italy
| | | | - Paola Granata
- SMeL specializzato Citogenetica e Genetica Medica, ASST Sette Laghi, Osp. di Circolo e Fond. Macchi, Varese, Italy
| | - Ilaria Longo
- U.O.C. Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Michela Malacarne
- Lab. di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | | | | | | | - Chiara Palka
- Dipartimento di Pediatria, Università G. D'Annunzio, Chieti-Pescara, Italy
| | - Vanna Pecile
- S.C. Genetica Medica, IRCCS Burlo Garofolo, Trieste, Italy
| | - Chiara Pessina
- SMeL specializzato Citogenetica e Genetica Medica, ASST Sette Laghi, Osp. di Circolo e Fond. Macchi, Varese, Italy
| | - Diana Postorivo
- U.O.C. Lab. di Genetica Medica, Policlinico Tor Vergata, Roma, Italy
| | - Serena Redaelli
- Dipartimento di Medicina e Chirurgia, Università di Milano-Bicocca, Monza, Italy
| | - Alessandra Renieri
- U.O.C. Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Chiara Rigon
- U.O.C. Genetica e Epidemiologia Clinica, A.O.U. di Padova, Padova, Italy
| | - Fabiola Tiberi
- A.O.U. Ospedali Riuniti Umberto I - G.M.Lancisi - G.Salesi, Lab. Genetica Medica SOS Malattie Rare, Ancona, Italy
| | - Mariella Tonelli
- LCGM Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italy
| | - Nicoletta Villa
- U.S. Genetica Medica, Ospedale San Gerardo ASST Monza, Monza, Italy
| | - Anna Zilio
- U.O.S. Genetica e Biologia Molecolare, Azienda ULSS 6, Vicenza, Italy
| | - Daniela Zuccarello
- U.O.C. Genetica e Epidemiologia Clinica, A.O.U. di Padova, Padova, Italy
| | - Antonio Novelli
- U.O.C. Laboratorio di Genetica Medica, Ospedale Pediatrico del Bambino Gesù, Roma, Italy
| | - Lidia Larizza
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Daniela Giardino
- Lab. di Citogenetica Medica, Istituto Auxologico Italiano, IRCCS, Milano, Italy
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Tsuchida N, Nakashima M, Kato M, Heyman E, Inui T, Haginoya K, Watanabe S, Chiyonobu T, Morimoto M, Ohta M, Kumakura A, Kubota M, Kumagai Y, Hamano SI, Lourenco CM, Yahaya NA, Ch'ng GS, Ngu LH, Fattal-Valevski A, Weisz Hubshman M, Orenstein N, Marom D, Cohen L, Goldberg-Stern H, Uchiyama Y, Imagawa E, Mizuguchi T, Takata A, Miyake N, Nakajima H, Saitsu H, Miyatake S, Matsumoto N. Detection of copy number variations in epilepsy using exome data. Clin Genet 2018; 93:577-587. [PMID: 28940419 DOI: 10.1111/cge.13144] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/12/2017] [Accepted: 09/17/2017] [Indexed: 12/14/2022]
Abstract
Epilepsies are common neurological disorders and genetic factors contribute to their pathogenesis. Copy number variations (CNVs) are increasingly recognized as an important etiology of many human diseases including epilepsy. Whole-exome sequencing (WES) is becoming a standard tool for detecting pathogenic mutations and has recently been applied to detecting CNVs. Here, we analyzed 294 families with epilepsy using WES, and focused on 168 families with no causative single nucleotide variants in known epilepsy-associated genes to further validate CNVs using 2 different CNV detection tools using WES data. We confirmed 18 pathogenic CNVs, and 2 deletions and 2 duplications at chr15q11.2 of clinically unknown significance. Of note, we were able to identify small CNVs less than 10 kb in size, which might be difficult to detect by conventional microarray. We revealed 2 cases with pathogenic CNVs that one of the 2 CNV detection tools failed to find, suggesting that using different CNV tools is recommended to increase diagnostic yield. Considering a relatively high discovery rate of CNVs (18 out of 168 families, 10.7%) and successful detection of CNV with <10 kb in size, CNV detection by WES may be able to surrogate, or at least complement, conventional microarray analysis.
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Affiliation(s)
- N Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - M Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - M Kato
- Department of Pediatrics, Yamagata University Faculty of Medicine, Yamagata, Japan.,Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - E Heyman
- Pediatric Neurology Department Pediatric Epilepsy Service, Assaf Harofeh Medical Center, Zerifin, Israel
| | - T Inui
- Department of Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - K Haginoya
- Department of Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - S Watanabe
- Department of Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - T Chiyonobu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - M Morimoto
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - M Ohta
- Department of Pediatrics, JA Toride General Hospital, Toride, Ibaraki, Japan
| | - A Kumakura
- Department of Pediatrics, Kitano Hospital, The Tazuke Kofukai Medical Research Institute, Osaka, Japan
| | - M Kubota
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan
| | - Y Kumagai
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - S-I Hamano
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - C M Lourenco
- Neurogenetics Unit, School of Medicine of Ribeirao Preto, University of Sao Paulo, Sao Paulo, Brazil
| | - N A Yahaya
- Hospital Raja Perempuan Zainab II, Kota Bharu, Malaysia
| | - G-S Ch'ng
- Genetic Department, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - L-H Ngu
- Genetic Department, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - A Fattal-Valevski
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Neurology Unit, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - M Weisz Hubshman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Raphael Recanati Genetics Institute, Rabin Medical Center, Petach Tikva, Israel
| | - N Orenstein
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - D Marom
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Pediatrics A, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - L Cohen
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - H Goldberg-Stern
- Epilepsy Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Y Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - E Imagawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - T Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - A Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - N Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - H Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - H Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - S Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - N Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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11
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Darouich S, Boutaud L, Bessières B, Bonnière M, Martinovic J, Mechler C, Alby C, Bernard JP, Roth P, Ville Y, Malan V, Vekemans M, Attié-Bitach T, Encha-Razavi F. Fetal Cerebral Ventricular Dilatation: Etiopathogenic Study of 130 Observations. Birth Defects Res 2017; 109:1586-1595. [DOI: 10.1002/bdr2.1093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/18/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Sihem Darouich
- Unité de Foetopathologie, Hôpital Universitaire Habib Bougatfa, Faculté de Médecine de Tunis; Université Tunis El Manar; Tunis Tunisie
| | - Lucile Boutaud
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes; Paris France
| | - Bettina Bessières
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Maryse Bonnière
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Jelena Martinovic
- Unité de Pathologie Fœtale; Hôpital Antoine Béclère, APHP; Paris France
| | - Charlotte Mechler
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Caroline Alby
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Jean-Pierre Bernard
- Service de Gynécologie-Obstétrique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Philippe Roth
- Service de Gynécologie-Obstétrique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Yves Ville
- Service de Gynécologie-Obstétrique; Hôpital Necker-Enfants Malades, APHP; Paris France
| | - Valerie Malan
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes; Paris France
| | - Michel Vekemans
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes; Paris France
| | - Tania Attié-Bitach
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
- INSERM U-1163, Institut Imagine; Hôpital Necker-Enfants Malades, APHP; Paris France
- Université Paris Descartes; Paris France
| | - Férechté Encha-Razavi
- Service d'Histologie-Embryologie-Cytogénétique; Hôpital Necker-Enfants Malades, APHP; Paris France
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12
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Chen CP, Lin SP, Chern SR, Wu PS, Chen YN, Chen SW, Lee CC, Town DD, Yang CW, Wang W. Molecular cytogenetic characterization of an inv dup(15) chromosome presenting as a small supernumerary marker chromosome associated with the inv dup(15) syndrome. Taiwan J Obstet Gynecol 2016; 55:728-732. [DOI: 10.1016/j.tjog.2016.06.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2016] [Indexed: 12/13/2022] Open
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13
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Oikonomakis V, Kosma K, Mitrakos A, Sofocleous C, Pervanidou P, Syrmou A, Pampanos A, Psoni S, Fryssira H, Kanavakis E, Kitsiou-Tzeli S, Tzetis M. Recurrent copy number variations as risk factors for autism spectrum disorders: analysis of the clinical implications. Clin Genet 2016; 89:708-18. [PMID: 26777411 DOI: 10.1111/cge.12740] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/08/2016] [Accepted: 01/13/2016] [Indexed: 12/31/2022]
Abstract
Chromosomal microarray analysis (CMA) is currently considered a first-tier diagnostic assay for the investigation of autism spectrum disorders (ASD), developmental delay and intellectual disability of unknown etiology. High-resolution arrays were utilized for the identification of copy number variations (CNVs) in 195 ASD patients of Greek origin (126 males, 69 females). CMA resulted in the detection of 65 CNVs, excluding the known polymorphic copy number polymorphisms also found in the Database of Genomic Variants, for 51/195 patients (26.1%). Parental DNA testing in 20/51 patients revealed that 17 CNVs were de novo, 6 paternal and 3 of maternal origin. The majority of the 65 CNVs were deletions (66.1%), of which 5 on the X-chromosome while the duplications, of which 7 on the X-chromosome, were rarer (22/65, 33.8%). Fifty-one CNVs from a total of 65, reported for our cohort of ASD patients, were of diagnostic significance and well described in the literature while 14 CNVs (8 losses, 6 gains) were characterized as variants of unknown significance and need further investigation. Among the 51 patients, 39 carried one CNV, 10 carried two CNVs and 2 carried three CNVs. The use of CMA, its clinical validity and utility was assessed.
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Affiliation(s)
- V Oikonomakis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - K Kosma
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Mitrakos
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - C Sofocleous
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.,Research Institute for the Study of Genetic and Malignant Diseases in Childhood, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - P Pervanidou
- 1st Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Syrmou
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Pampanos
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.,Department of Genetics, "Alexandra" University Maternal Hospital, Athens, Greece
| | - S Psoni
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - H Fryssira
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - E Kanavakis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.,Research Institute for the Study of Genetic and Malignant Diseases in Childhood, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - S Kitsiou-Tzeli
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Tzetis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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