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Tolezano GC, Bastos GC, da Costa SS, Freire BL, Homma TK, Honjo RS, Yamamoto GL, Passos-Bueno MR, Koiffmann CP, Kim CA, Vianna-Morgante AM, de Lima Jorge AA, Bertola DR, Rosenberg C, Krepischi ACV. Burden of Rare Copy Number Variants in Microcephaly: A Brazilian Cohort of 185 Microcephalic Patients and Review of the Literature. J Autism Dev Disord 2024; 54:1181-1212. [PMID: 36502452 DOI: 10.1007/s10803-022-05853-z] [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] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
Microcephaly presents heterogeneous genetic etiology linked to several neurodevelopmental disorders (NDD). Copy number variants (CNVs) are a causal mechanism of microcephaly whose investigation is a crucial step for unraveling its molecular basis. Our purpose was to investigate the burden of rare CNVs in microcephalic individuals and to review genes and CNV syndromes associated with microcephaly. We performed chromosomal microarray analysis (CMA) in 185 Brazilian patients with microcephaly and evaluated microcephalic patients carrying < 200 kb CNVs documented in the DECIPHER database. Additionally, we reviewed known genes and CNV syndromes causally linked to microcephaly through the PubMed, OMIM, DECIPHER, and ClinGen databases. Rare clinically relevant CNVs were detected in 39 out of the 185 Brazilian patients investigated by CMA (21%). In 31 among the 60 DECIPHER patients carrying < 200 kb CNVs, at least one known microcephaly gene was observed. Overall, four gene sets implicated in microcephaly were disclosed: known microcephaly genes; genes with supporting evidence of association with microcephaly; known macrocephaly genes; and novel candidates, including OTUD7A, BBC3, CNTN6, and NAA15. In the review, we compiled 957 known microcephaly genes and 58 genomic CNV loci, comprising 13 duplications and 50 deletions, which have already been associated with clinical findings including microcephaly. We reviewed genes and CNV syndromes previously associated with microcephaly, reinforced the high CMA diagnostic yield for this condition, pinpointed novel candidate loci linked to microcephaly deserving further evaluation, and provided a useful resource for future research on the field of neurodevelopment.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Bruna Lucheze Freire
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Thais Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Celia Priszkulnik Koiffmann
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Angela Maria Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
- Institute of Biosciences, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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2
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Jouret G, Egloff M, Landais E, Tassy O, Giuliano F, Karmous-Benailly H, Coutton C, Satre V, Devillard F, Dieterich K, Vieville G, Kuentz P, le Caignec C, Beneteau C, Isidor B, Nizon M, Callier P, Marquet V, Bieth E, Lévy J, Tabet AC, Lyonnet S, Baujat G, Rio M, Cartault F, Scheidecker S, Gouronc A, Schalk A, Jacquin C, Spodenkiewicz M, Angélini C, Pennamen P, Rooryck C, Doco-Fenzy M, Poirsier C. Clinical and genomic delineation of the new proximal 19p13.3 microduplication syndrome. Am J Med Genet A 2023; 191:52-63. [PMID: 36196855 DOI: 10.1002/ajmg.a.62983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
Abstract
A small but growing body of scientific literature is emerging about clinical findings in patients with 19p13.3 microdeletion or duplication. Recently, a proximal 19p13.3 microduplication syndrome was described, associated with growth delay, microcephaly, psychomotor delay and dysmorphic features. The aim of our study was to better characterize the syndrome associated with duplications in the proximal 19p13.3 region (prox 19p13.3 dup), and to propose a comprehensive analysis of the underlying genomic mechanism. We report the largest cohort of patients with prox 19p13.3 dup through a collaborative study. We collected 24 new patients with terminal or interstitial 19p13.3 duplication characterized by array-based Comparative Genomic Hybridization (aCGH). We performed mapping, phenotype-genotype correlations analysis, critical region delineation and explored three-dimensional chromatin interactions by analyzing Topologically Associating Domains (TADs). We define a new 377 kb critical region (CR 1) in chr19: 3,116,922-3,494,377, GRCh37, different from the previously described critical region (CR 2). The new 377 kb CR 1 includes a TAD boundary and two enhancers whose common target is PIAS4. We hypothesize that duplications of CR 1 are responsible for tridimensional structural abnormalities by TAD disruption and misregulation of genes essentials for the control of head circumference during development, by breaking down the interactions between enhancers and the corresponding targeted gene.
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Affiliation(s)
- Guillaume Jouret
- Department of Genetics, Reims University Hospital, Reims, France.,National Center of Genetics (NCG), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Matthieu Egloff
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France
| | - Emilie Landais
- Department of Genetics, Reims University Hospital, Reims, France
| | | | | | | | - Charles Coutton
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France.,ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France
| | - Véronique Satre
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Françoise Devillard
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Klaus Dieterich
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Gaëlle Vieville
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Paul Kuentz
- Génétique Biologique, PCBio, Besançon University Hospital, Besançon, France
| | - Cédric le Caignec
- ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,Department of Genetics, Nantes University Hospital, Nantes, France
| | - Claire Beneteau
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Bertrand Isidor
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Mathilde Nizon
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Patrick Callier
- ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,Department of Genetics, Dijon University Hospital, Dijon, France
| | - Valentine Marquet
- ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,Department of Genetics, Limoges University Hospital, Limoges, France
| | - Eric Bieth
- Department of Genetics, Toulouse University Hospital, Toulouse, France
| | - Jonathan Lévy
- Department of Genetics, Robert-Debré University Hospital, Paris, France
| | - Anne-Claude Tabet
- Department of Genetics, Robert-Debré University Hospital, Paris, France
| | - Stanislas Lyonnet
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France.,INSERM U-1163, Université de Paris, Paris, France
| | - Geneviève Baujat
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France
| | - Marlène Rio
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France
| | - François Cartault
- Department of Genetics, La Réunion University Hospital, Saint Denis, France
| | | | | | | | - Clémence Jacquin
- Department of Genetics, Reims University Hospital, Reims, France
| | | | - Chloé Angélini
- CHU Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | | | | | - Martine Doco-Fenzy
- Department of Genetics, Reims University Hospital, Reims, France.,ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,EA3801, SFR CAPSANTE, Reims, France
| | - Céline Poirsier
- Department of Genetics, Reims University Hospital, Reims, France
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Bastos GC, Tolezano GC, Krepischi ACV. Rare CNVs and Known Genes Linked to Macrocephaly: Review of Genomic Loci and Promising Candidate Genes. Genes (Basel) 2022; 13:genes13122285. [PMID: 36553552 PMCID: PMC9778424 DOI: 10.3390/genes13122285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Macrocephaly frequently occurs in single-gene disorders affecting the PI3K-AKT-MTOR pathway; however, epigenetic mutations, mosaicism, and copy number variations (CNVs) are emerging relevant causative factors, revealing a higher genetic heterogeneity than previously expected. The aim of this study was to investigate the role of rare CNVs in patients with macrocephaly and review genomic loci and known genes. We retrieved from the DECIPHER database de novo <500 kb CNVs reported on patients with macrocephaly; in four cases, a candidate gene for macrocephaly could be pinpointed: a known microcephaly gene-TRAPPC9, and three genes based on their functional roles-RALGAPB, RBMS3, and ZDHHC14. From the literature review, 28 pathogenic CNV genomic loci and over 300 known genes linked to macrocephaly were gathered. Among the genomic regions, 17 CNV loci (~61%) exhibited mirror phenotypes, that is, deletions and duplications having opposite effects on head size. Identifying structural variants affecting head size can be a preeminent source of information about pathways underlying brain development. In this study, we reviewed these genes and recurrent CNV loci associated with macrocephaly, as well as suggested novel potential candidate genes deserving further studies to endorse their involvement with this phenotype.
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AYAZ A, GEZDIRICI A, YILMAZ GULEC E, OZALP Ö, KOSEOGLU AH, DOGRU Z, YALCINTEPE S. Diagnostic Value of Microarray Method in Autism Spectrum Disorder, Intellectual Disability, and Multiple Congenital Anomalies and Some Candidate Genes for Autism: Experience of Two Centers. Medeni Med J 2022; 37:180-193. [PMID: 35735171 PMCID: PMC9234369 DOI: 10.4274/mmj.galenos.2022.70962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Objective: This study aimed to demonstrate the diagnostic value of microarray testing in autism spectrum disorder, intellectual disability, and multiple congenital anomalies of unknown etiology, as well as to report some potential candidate genes for autism. Methods: Microarray analysis records between January 2016 and December 2017 from two Genetic Diagnostic Centers in Turkey, Kanuni Sultan Suleyman and Adana Numune Training and Research Hospital, were compiled. Detected copy number variations (CNVs) were classified as benign, likely benign, variants of uncertain significance (VUS), likely pathogenic, and pathogenic according to American College of Medical Genetics and Genomics guidelines. The clinical findings of the some patients and the literature data were compared. Results: In 109 (24.5%) of 445 patients, a total of 163 CNVs with reporting criterion feature were detected. Sixty-nine (42%) and 8 (5%) of these were evaluated as pathogenic and likely pathogenic, respectively. Fifteen (9%) CNVs were also evaluated as VUS. Pathogenic or likely pathogenic CNVs were detected in 61 (13.6%) of 445 patients. Conclusions: We found that the probability of elucidating the etiology of microarray method in autism spectrum disorder, intellectual disability, and multiple congenital anomalies is 13.6% with a percentage similar to the literature. We suggest that the MYT1L, PXDN, TPO, and AUTS2 genes are all strong candidate genes for autism spectrum disorders. We detailed the clinical findings of the cases and reported that some CNV regions in the genome may be associated with autism.
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Gu C, Gao H, Li K, Dai X, Yang Z, Li R, Wen C, He Y. Copy Number Variation Analysis of Euploid Pregnancy Loss. Front Genet 2022; 13:766492. [PMID: 35401693 PMCID: PMC8984164 DOI: 10.3389/fgene.2022.766492] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/24/2022] [Indexed: 12/30/2022] Open
Abstract
Objectives: Copy number variant (CNV) is believed to be the potential genetic cause of pregnancy loss. However, CNVs less than 3 Mb in euploid products of conceptions (POCs) remain largely unexplored. The aim of this study was to investigate the features of CNVs less than 3 Mb in POCs and their potential clinical significance in pregnancy loss/fetal death.Methods: CNV data were extracted from a cohort in our institution and 19 peer-reviewed publications, and only those CNVs less than 3 Mb detected in euploid pregnancy loss/fetal death were included. We conducted a CNV map to analyze the distribution of CNVs in chromosomes using R packages karyoploteR_1.10.5. Gene names and annotated gene types covered by those CNVs were mined from the human Release 19 reference genome file and GENECODE database. We assessed the expression patterns and the consequences of murine knock-out of those genes using TiGER and Mouse Genome Informatics (MGI) databases. Functional enrichment and pathway analysis for genes in CNVs were performed using clusterProfiler V3.12.0.Result: Breakpoints of 564 CNVs less than 3 Mb were obtained from 442 euploid POCs, with 349 gains and 185 losses. The CNV map showed that CNVs were distributed in all chromosomes, with the highest frequency detected in chromosome 22 and the lowest frequency in chromosome Y, and CNVs showed a higher density in the pericentromeric and sub-telomeric regions. A total of 5,414 genes mined from the CNV regions (CNVRs), Gene Ontology (GO), and pathway analysis showed that the genes were significantly enriched in multiple terms, especially in sensory perception, membrane region, and tight junction. A total of 995 protein-coding genes have been reported to present mammalian phenotypes in MGI, and 276 of them lead to embryonic lethality or abnormal embryo/placenta in knock-out mouse models. CNV located at 19p13.3 was the most common CNV of all POCs.Conclusion: CNVs less than 3 Mb in euploid POCs distribute unevenly in all chromosomes, and a higher density was seen in the pericentromeric and sub-telomeric regions. The genes in those CNVRs are significantly enriched in biological processes and pathways that are important to embryonic/fetal development. CNV in 19p13.3 and the variations of ARID3A and FSTL3 might contribute to pregnancy loss.
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Affiliation(s)
- Chongjuan Gu
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huan Gao
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Kuanrong Li
- Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xinyu Dai
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zhao Yang
- West China Hospital, Sichuan University, Chengdu, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Canliang Wen
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yaojuan He
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Yaojuan He,
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Martínez Anaya D, Fernández Hernández L, González Del Angel A, Alcántara Ortigoza MA, Ulloa Avilés V, Pérez Vera P. Nonmosaic Trisomy 19p13.3p13.2 Resulting from a Rare Unbalanced t(Y;19)(q12;p13.2) Translocation in a Patient with Pachygyria and Polymicrogyria. Cytogenet Genome Res 2020; 160:177-184. [PMID: 32369810 DOI: 10.1159/000507561] [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: 01/21/2020] [Accepted: 03/18/2020] [Indexed: 11/19/2022] Open
Abstract
Nonmosaic trisomy involving 19p13.3p13.2 is a very uncommon abnormality. At present, only 12 cases with this genetic condition have been reported in the literature. However, the size of the trisomic fragment is heterogeneous and thus, the clinical spectrum is variable. Herein, we report the clinical and cytogenetic characterization of a 5-year-old boy with nonmosaic trisomy 19p13.3p13.2 (7.38 Mb), generated by a derivative Y chromosome resulting from a de novo unbalanced translocation t(Y;19)(q12;p13.2). We demonstrated the integrity of the euchromatic regions in the abnormal Y chromosome to confirm the pure trisomy 19p. Our patient shares some clinical features described in other reported patients with pure trisomy 19p, such as craniofacial anomalies, developmental delay, and heart defects. Different to previous reports, our case exhibits frontal pachygyria and polymicrogyria. These additional features contribute to further delineate the clinical spectrum of trisomy 19p13.3p13.2.
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7
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Tenorio J, Nevado J, González-Meneses A, Arias P, Dapía I, Venegas-Vega CA, Calvente M, Hernández A, Landera L, Ramos S, Cigudosa JC, Pérez-Jurado LA, Lapunzina P. Further definition of the proximal 19p13.3 microdeletion/microduplication syndrome and implication of PIAS4 as the major contributor. Clin Genet 2020; 97:467-476. [PMID: 31972898 DOI: 10.1111/cge.13689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/24/2019] [Accepted: 11/01/2019] [Indexed: 12/15/2022]
Abstract
The proximal 19p13.3 microdeletion/microduplication (prox19p13.3del/dup) syndrome is a recently described disorder with common clinical features including developmental delay, intellectual disability, speech delay, facial dysmorphic features with ear defects, anomalies of the hands and feet, umbilical hernia and hypotonia. While deletions are associated with macrocephaly, patients with duplications have microcephaly. The smallest region of overlap in multiple patients (113.5 kb) included three genes and one pseudogene, with a suggested major role of PIAS4 in determination of the phenotype and head size in these patients. Here, we refine the prox19p13.3del/dup with four additional patients: two with microdeletions, one with microduplication and one family with single-nucleotide nonsense variant in PIAS4. The patient with the PIAS4 loss of function variant displayed a phenotype quite similar to deletion patients -including the macrocephaly and many other core features of the syndrome. Patient's SNV was inherited from her mother who is similarly affected. Thus, our data indicate that PIAS4 is a major contributor to the proximal 19p13.3del/dup syndrome phenotype. In summary, we report the first patient with a pathogenic variant in PIAS4- and three additional rearrangements at the proximal 19p13.3 locus. These observations add further evidence about the molecular basis of this microdeletion/microduplication syndrome.
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Affiliation(s)
- Jair Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,ERN-ITHACA, ITHACA European Reference Network
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,ERN-ITHACA, ITHACA European Reference Network
| | - Antonio González-Meneses
- Dysmorphology and Metabolism unit, Hospital Universitario Virgen del Rocío, Av. Manuel Siurot, Sevilla, Spain
| | - Pedro Arias
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | - Irene Dapía
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | - Carlos A Venegas-Vega
- Unidadde Genética, Hospital General de México, México City, Mexico, Facultad deMedicina, Universidad Nacional Autónoma de México, México City, Mexico
| | - María Calvente
- NIMGENETICS, c/ Faraday, 7 Parque Científico de Madrid, Madrid, Spain
| | - Alicia Hernández
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | - Leandro Landera
- Congenital Malformations Laboratory, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho, Rio deJaneiro, Brazil
| | - Sergio Ramos
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
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- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | | | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra, and IMIM-Hospital del Mar, Barcelona, Spain.,Women's and Children's Hospital, South Australian Health and Medical Research Institute (SAHMRI), The University of Adelaide, Adelaide, Australia
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,ERN-ITHACA, ITHACA European Reference Network
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8
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Viñas-Jornet M, Esteba-Castillo S, Baena N, Ribas-Vidal N, Ruiz A, Torrents-Rodas D, Gabau E, Vilella E, Martorell L, Armengol L, Novell R, Guitart M. High Incidence of Copy Number Variants in Adults with Intellectual Disability and Co-morbid Psychiatric Disorders. Behav Genet 2018; 48:323-336. [PMID: 29882083 PMCID: PMC6028865 DOI: 10.1007/s10519-018-9902-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 05/10/2018] [Indexed: 01/04/2023]
Abstract
A genetic analysis of unexplained mild-moderate intellectual disability and co-morbid psychiatric or behavioural disorders is not systematically conducted in adults. A cohort of 100 adult patients affected by both phenotypes were analysed in order to identify the presence of copy number variants (CNVs) responsible for their condition identifying a yield of 12.8% of pathogenic CNVs (19% when including clinically recognizable microdeletion syndromes). Moreover, there is a detailed clinical description of an additional 11% of the patients harbouring possible pathogenic CNVs—including a 7q31 deletion (IMMP2L) in two unrelated patients and duplications in 3q29, 9p24.2p24.1 and 15q14q15.1—providing new evidence of its contribution to the phenotype. This study adds further proof of including chromosomal microarray analysis (CMA) as a mandatory test to improve the diagnosis in the adult patients in psychiatric services.
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Affiliation(s)
- Marina Viñas-Jornet
- Genetics lab, UDIAT-centre diagnostic. Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, C/Parc Tauli,1, 08208, Sabadell, Barcelona, Spain.,Cellular Biology, Physiology and Immunology Department, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Susanna Esteba-Castillo
- Mental Health and Intellectual Disability Specialized Service, Institut Assistència Sanitària (IAS), Parc Hospitalari Martí i Julià, Girona, Spain
| | - Neus Baena
- Genetics lab, UDIAT-centre diagnostic. Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, C/Parc Tauli,1, 08208, Sabadell, Barcelona, Spain
| | - Núria Ribas-Vidal
- Mental Health and Intellectual Disability Specialized Service, Institut Assistència Sanitària (IAS), Parc Hospitalari Martí i Julià, Girona, Spain
| | - Anna Ruiz
- Genetics lab, UDIAT-centre diagnostic. Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, C/Parc Tauli,1, 08208, Sabadell, Barcelona, Spain
| | - David Torrents-Rodas
- Mental Health and Intellectual Disability Specialized Service, Institut Assistència Sanitària (IAS), Parc Hospitalari Martí i Julià, Girona, Spain
| | - Elisabeth Gabau
- Pediatry-Clinical Genetics Service, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, CIBERSAM, Reus, Spain
| | - Lourdes Martorell
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, CIBERSAM, Reus, Spain
| | - Lluís Armengol
- Research and Development Department, qGenomics Laboratory, Barcelona, Spain
| | - Ramon Novell
- Mental Health and Intellectual Disability Specialized Service, Institut Assistència Sanitària (IAS), Parc Hospitalari Martí i Julià, Girona, Spain
| | - Míriam Guitart
- Genetics lab, UDIAT-centre diagnostic. Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, C/Parc Tauli,1, 08208, Sabadell, Barcelona, Spain.
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Efficient strategy for the molecular diagnosis of intractable early-onset epilepsy using targeted gene sequencing. BMC Med Genomics 2018; 11:6. [PMID: 29390993 PMCID: PMC5796507 DOI: 10.1186/s12920-018-0320-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 01/03/2018] [Indexed: 11/22/2022] Open
Abstract
Background We intended to evaluate diagnostic utility of a targeted gene sequencing by using next generation sequencing (NGS) panel in patients with intractable early-onset epilepsy (EOE) and find the efficient analytical step for increasing the diagnosis rate. Methods We assessed 74 patients with EOE whose seizures started before 3 years of age using a customized NGS panel that included 172 genes. Single nucleotide variants (SNVs) and exonic and chromosomal copy number variations (CNVs) were intensively examined with our customized pipeline and crosschecked with commercial or pre-built software. Variants were filtered and prioritized by in-depth clinical review, and finally classified according to the American College of Medical Genetics and Genomics guidelines. Each case was further discussed in a monthly consensus meeting that included the participation of all laboratory personnel, bioinformaticians, geneticists, and clinicians. Results The NGS panel identified 28 patients (37.8%) with genetic abnormalities; 25 patients had pathogenic or likely pathogenic SNVs in 17 genes including SXTBP1 (n = 3), CDKL5 (n = 2), KCNQ2 (n = 2), SCN1A (n = 2), SYNGAP1 (n = 2), GNAO1 (n = 2), KCNT1 (n = 2), BRAT1, WWOX, ZEB2, CHD2, PRICKLE2, COL4A1, DNM1, SCN8A, MECP2, SLC9A6 (n = 1). The other 3 patients had pathogenic CNVs (2 duplications and 1 deletion) with varying sizes (from 2.5 Mb to 12 Mb). The overall diagnostic yield was 37.8% after following our step-by-step approach for clinical consensus. Conclusions NGS is a useful diagnostic tool with great utility for patients with EOE. Diagnostic yields can be maximized with a standardized and team-based approach. Electronic supplementary material The online version of this article (10.1186/s12920-018-0320-7) contains supplementary material, which is available to authorized users.
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Novikova I, Sen P, Manzardo A, Butler MG. Duplication of 19p13.3 in 11-Year-Old Male Patient with Dysmorphic Features and Intellectual Disability: A Review. J Pediatr Genet 2017; 6:227-233. [PMID: 29142765 PMCID: PMC5683958 DOI: 10.1055/s-0037-1603650] [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] [Received: 02/28/2017] [Accepted: 04/28/2017] [Indexed: 12/15/2022]
Abstract
We present a clinical report of an 11-year-old male patient with an interstitial duplication of 19p13.3 (829 kb in size) at genomic coordinates 3,804,495-4,033,722 bp (hg19) identified by chromosomal microarray analysis and review the literature from nine published reports adding knowledge regarding this chromosomal anomaly and clinical outcomes. The size of the duplication ranged from 0.83 to 8.9 Mb in the nine individuals. The young boy in our report was dysmorphic with microcephaly, abnormal craniofacial features, intellectual disability, aggression, and a heart murmur. All patients were found to have a psychomotor developmental delay and/or intellectual disability with the majority having microcephaly, intrauterine growth retardation, and hypotonia. Common craniofacial findings included a tall, prominent forehead, an elongated face, epicanthal folds, hypertelorism, prominent low-set ears, philtrum anomaly, and a small mouth. Other less common features included abnormal digits, sparse hair, and cardiac defects. Clinical features, chromosome duplication sizes, locations, and the number of genes will be summarized in a tabular form.
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Affiliation(s)
- Irina Novikova
- Departments of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, United States
| | - Paushpala Sen
- Departments of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, United States
| | - Ann Manzardo
- Departments of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, United States
| | - Merlin G. Butler
- Departments of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, United States
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Šumanović-Glamuzina D, Lozić B, Iwanowski PS, Zemunik T, Bilinovac Z, Stasiewicz-Jarocka B, Panasiuk B, Midro AT. Limited survivability of unbalanced progeny of carriers of a unique t(4;19)(p15.32;p13.3): a study in multiple generations. Mol Cytogenet 2017; 10:29. [PMID: 28785312 PMCID: PMC5545035 DOI: 10.1186/s13039-017-0330-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/26/2017] [Indexed: 11/22/2022] Open
Abstract
Background Carriership of a reciprocal chromosomal translocation (RCT) involving the short arm of chromosome 4 (4p) may result in birth of a child with Wolf-Hirschhorn syndrome (WHS) due to monosomy 4p, a priori modified by the impact of the partner chromosome imbalance. Familial transmission studies of RCT enable obtaining empirical risk figures that are essential for genetic counseling. In this study, pedigree data from carriers of a unique t(4;19)(p15.32;p13.3), ascertained by two children with WHS phenotype, were collected through five generations and empirical risk for different pregnancy outcomes was assessed. In addition, the phenotype-karyotype correlation was studied in two unbalanced children against the phenotypes of children (literature data) with pure monosomy 4p15.32 → pter and pure trisomy 19p13.3 → pter, accordingly. The phenotype analysis was conducted using the catalogue of traits according to the Munich Dysmorphology Database. Pedigree segregation analysis was conducted by the direct method according to Stengel- Rutkowski et al. Results A double segment imbalance, trisomy 19p13.3 → pter with monosomy 4p15.32 → pter, was diagnosed in WHS progeny at birth. No essential modification of WHS phenotype by the additional trisomy 19p was observed, except for a limited survivability (death in infancy). Pedigree segregation analysis covered 39 relatives showed the probability rate for liveborn with unbalanced karyotype of 3.7 ± 3.6% (1/27), for stillbirth/neonatal death at 7.4 ± 5.0% (2/27), for miscarriage at 22.2 ± 8.0% (6/27), for the chance of having a baby without unbalanced karyotype was estimated at 66.7 ± 9.1% (18/27). In addition, the value of 7.4% for genetic counseling for any carrier of RCT at risk for single segment 19p13.3 → pter imbalance at birth was evaluated as such value have not been estimated so far. Conclusion Carriership of a t(4;19)(p15.32;p13.3) is at low risk for an unbalanced child at birth and for stillbirth/neonatal death but high for miscarriages. The chance of having a baby without unbalanced karyotype was estimated to be high. Monosomy 4p15.32 → pter together with trisomy 19p13.3 → pter as a double segment imbalance in children with WHS may be connected with a limited survivability in infancy. Electronic supplementary material The online version of this article (doi:10.1186/s13039-017-0330-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Bernarda Lozić
- Department of Pediatrics, University Hospital Centre Split, Split, Croatia
| | - Piotr S Iwanowski
- Department of Clinical Genetics, Medical University of Bialystok, Waszyngtona St. 13, PO Box 22, 15-089 Białystok, Poland
| | - Tatijana Zemunik
- Department of Medical Biology, School of Medicine Split, University of Split, Split, Croatia
| | - Zeljka Bilinovac
- Department of Pediatrics, University Hospital Mostar, Mostar, Bosnia and Herzegovina
| | - Beata Stasiewicz-Jarocka
- Department of Clinical Genetics, Medical University of Bialystok, Waszyngtona St. 13, PO Box 22, 15-089 Białystok, Poland
| | - Barbara Panasiuk
- Department of Clinical Genetics, Medical University of Bialystok, Waszyngtona St. 13, PO Box 22, 15-089 Białystok, Poland
| | - Alina T Midro
- Department of Clinical Genetics, Medical University of Bialystok, Waszyngtona St. 13, PO Box 22, 15-089 Białystok, Poland
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