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Wang Y, Bi S, Shi X, Dai L. Optical Genome Mapping Identifies a Novel Unbalanced Translocation Between Chromosomes 4q and 6q Leading to Feeding Difficulties and Hypotonia in a Neonate: A Case Report. Appl Clin Genet 2024; 17:63-69. [PMID: 38828444 PMCID: PMC11141715 DOI: 10.2147/tacg.s465244] [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: 02/21/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Optical Genome Mapping (OGM) technology has garnered growing interest for the identification of chromosomal structural variations (SVs), particularly complex ones that are implicated in genetic diseases in humans. In this study, we performed genetic diagnostics on a neonatal patient who presented with feeding difficulties, hypotonia, and an atrial septal defect. We utilized a combination of trio-whole exome sequencing and OGM for our analysis. The results revealed an unbalanced translocation between maternal chromosomes 4 and 6 in the proband, ogm[GRch38]t(4:6)(q35.2;q25.3), resulting in a 2.8 Mb deletion at the 4q35 terminal and a 10.2 Mb duplication at the 6q25 terminal. In summary, this study highlights how OGM, in conjunction with other genetic approaches, can unveil the genetic etiology of complex clinical syndromes. Neonatal patients often exhibit low specific phenotypes, underlining the significance of SV detection.
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Affiliation(s)
- Ying Wang
- Division of Neonatology, Anhui Provincial Children’s Hospital, Hefei, Anhui, 230051, People’s Republic of China
| | - Shaohua Bi
- Division of Neonatology, Anhui Provincial Children’s Hospital, Hefei, Anhui, 230051, People’s Republic of China
| | - Xiaoqing Shi
- Division of Neonatology, Anhui Provincial Children’s Hospital, Hefei, Anhui, 230051, People’s Republic of China
| | - Liying Dai
- Division of Neonatology, Anhui Provincial Children’s Hospital, Hefei, Anhui, 230051, People’s Republic of China
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Zhuang J, Liu S, Chen X, Jiang Y, Chen C. Identification of a novel isolated 4q35.2 microdeletion in a Chinese pediatric patient using chromosomal microarray analysis: a case report and literature review. Mol Cytogenet 2023; 16:18. [PMID: 37533110 PMCID: PMC10399047 DOI: 10.1186/s13039-023-00651-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Isolated terminal 4q35.2 microdeletion is an extremely rare copy number variant affecting people all over the world. To date, researchers still have controversial opinions and results on its pathogenicity. Here, we aim to present a Chinese pediatric patient with terminal 4q35.2 microdeletion and use this case to clarify the underlying genotype-phenotype correlation. METHODS A 17-year-old boy from Quanzhou, South China, was recruited as the main subject in this study. Karyotype and single-nucleotide polymorphism (SNP) based microarray analysis were carried out to detect chromosomal abnormalities and copy number variants in this family. Trio whole exome sequencing (Trio-WES) was performed to investigate the potential pathogenic variant in this family. RESULTS During observation, we identified abnormal clinical phenotypes including upper eyelid ptosis, motor developmental delay, abnormal posturing, abnormality of coordination, attention deficit hyperactivity disorder, and involuntary movements in the patient. SNP array analysis results confirmed a case of 2.0 Mb 4q35.2 microdeletion and parental SNP array verification results indicated that the terminal 4q35.2 microdeletion was inherited from his mother. No copy number variants were detected in his father. In addition, the trio-WES results demonstrated none of pathogenic or likely pathogenic variants in the patient. CONCLUSIONS This study brings a novel analysis of a case of 2.0 Mb terminal 4q35.2 microdeletion affecting a Chinese individual. In addition, additional clinical symptoms such as upper eyelid ptosis and involuntary movements were first reported to affect a patient with terminal 4q35.2 microdeletion, which may broaden the phenotype spectrum of the condition.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, People's Republic of China.
| | - Shufen Liu
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, People's Republic of China
| | - Xinying Chen
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, People's Republic of China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, People's Republic of China.
| | - Chunnuan Chen
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, People's Republic of China.
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de la Morena-Barrio B, Palomo Á, Padilla J, Martín-Fernández L, Rojo-Carrillo JJ, Cifuentes R, Bravo-Pérez C, Garrido-Rodríguez P, Miñano A, Rubio AM, Pagán J, Llamas M, Vicente V, Vidal F, Lozano ML, Corral J, de la Morena-Barrio ME. Impact of genetic structural variants in factor XI deficiency: identification, accurate characterization, and inferred mechanism by long-read sequencing. J Thromb Haemost 2023; 21:1779-1788. [PMID: 36940803 DOI: 10.1016/j.jtha.2023.03.009] [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: 12/23/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/23/2023]
Abstract
BACKGROUND Congenital factor XI (FXI) deficiency is a probably underestimated coagulopathy that confers antithrombotic protection. Characterization of genetic defects in F11 is mainly focused on the identification of single-nucleotide variants and small insertion/deletions because they represent up to 99% of the alterations accounting for factor deficiency, with only 3 gross gene defects of structural variants (SVs) having been described. OBJECTIVES To identify and characterize the SVs affecting F11. METHODS The study was performed in 93 unrelated subjects with FXI deficiency recruited in Spanish hospitals over a period of 25 years (1997-2022). F11 was analyzed by next-generation sequencing, multiplex ligand probe amplification, and long-read sequencing. RESULTS Our study identified 30 different genetic variants. Interestingly, we found 3 SVs, all heterozygous: a complex duplication affecting exons 8 and 9, a tandem duplication of exon 14, and a large deletion affecting the whole gene. Nucleotide resolution obtained by long-read sequencing revealed Alu repetitive elements involved in all breakpoints. The large deletion was probably generated de novo in the paternal allele during gametogenesis, and despite affecting 30 additional genes, no syndromic features were described. CONCLUSION SVs may account for a high proportion of F11 genetic defects implicated in the molecular pathology of congenital FXI deficiency. These SVs, likely caused by a nonallelic homologous recombination involving repetitive elements, are heterogeneous in both type and length and may be de novo. These data support the inclusion of methods to detect SVs in this disorder, with long-read-based methods being the most appropriate because they detect all SVs and achieve adequate nucleotide resolution.
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Affiliation(s)
- Belén de la Morena-Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Ángeles Palomo
- Servicio de Hematología y Hemoterapia del centro Materno-Infantil del Hospital Regional Universitario Carlos de Haya, Málaga, Spain
| | - José Padilla
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Laura Martín-Fernández
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain; Medicina Transfusional. Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan José Rojo-Carrillo
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Rosa Cifuentes
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Carlos Bravo-Pérez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Pedro Garrido-Rodríguez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Antonia Miñano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Ana María Rubio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Javier Pagán
- Servicio de Medicina Interna, Hospital Universitario Morales Meseguer, Murcia, Spain
| | - María Llamas
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Vicente Vicente
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Francisco Vidal
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain; Medicina Transfusional. Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - María Luisa Lozano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Javier Corral
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain.
| | - María Eugenia de la Morena-Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain.
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Song J, Jiang W, Zhang C, Wang B. Prenatal diagnosis and genetic counseling of a 10p11.23q11.21 duplication associated with normal phenotype. Mol Cytogenet 2022; 15:21. [PMID: 35659699 PMCID: PMC9164483 DOI: 10.1186/s13039-022-00598-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background Copy number variants (CNVs) are an important source of normal and pathogenic genome variations. Unbalanced chromosome abnormalities (UBCA) are either gains or losses or large genomic regions, but the affected person is not or only minimally clinically affected. CNVs and UBCA identified in prenatal cases need careful considerations and correct interpretation if those are harmless or harmful variants from the norm. Case presentation A 24-year-old, gravida 1, para 0, woman underwent amniocentesis at 17 weeks of gestation because the noninvasive prenatal testing (NIPT) results revealed a 12.4 Mb duplication from 10p11.2 to 10q11.2. GTG-banding karyotype analysis was performed on cultured amniocytes. Chromosomal microarray analysis (CMA) on uncultured amniocytes was performed. Results Chromosomal GTG-banding of the cultured amniocytes revealed a karyotype of 46,XX,dup(10)(p11.2q11.2). CMA detected a 12.5-Mb chromosomal duplication in the region of 10p11.23q11.21 (arr[GRCh37] 10p11.23q11.21(30,345,109_42,826,062) × 3). Conclusion The present report enlarges the known UBCA region 10p11.22-10q11.22 to 10p11.23-10q11.22. Also it highlights that an integration of prenatal ultrasound, NIPT, karyotype analysis, CMA and genetic counseling is helpful for the prenatal diagnosis of chromosomal deletions/duplications.
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Affiliation(s)
- Jieping Song
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - Wei Jiang
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - Chengcheng Zhang
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - Bo Wang
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, People's Republic of China.
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Genotype–Phenotype Correlations for Putative Haploinsufficient Genes in Deletions of 6q26-q27: Report of Eight Patients and Review of Literature. Glob Med Genet 2022; 9:166-174. [PMID: 35707784 PMCID: PMC9192176 DOI: 10.1055/s-0042-1743568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/11/2022] [Indexed: 11/06/2022] Open
Abstract
Background
Cytogenomic analyses have been used to detect pathogenic copy number variants. Patients with deletions at 6q26-q27 present variable clinical features. We reported clinical and cytogenomic findings of eight unrelated patients with a deletion of 6q26-q27. A systematic review of the literature found 28 patients with a deletion of 6q26-q27 from 2010 to 2020.
Results
For these 36 patients, the sex ratio showed equal occurrence between males and females; 29 patients (81%) had a terminal deletion and seven patients (19%) had a proximal or distal interstitial deletion. Of the 22 patients with parental studies, deletions of de novo, maternal, paternal, and bi-parental inheritance accounted for 64, 18, 14, and 4% of patients, respectively. The most common clinical findings were brain abnormalities (100%) in fetuses observed by ultrasonography followed by developmental delay and intellectual disability (81%), brain abnormalities (72%), facial dysmorphism (66%), hypotonia (63%), learning difficulty or language delay (50%), and seizures (47%) in pediatric and adult patients. Anti-epilepsy treatment showed the effect on controlling seizures in these patients. Cytogenomic mapping defined one proximal critical region at 6q26 containing the putative haploinsufficient gene
PRKN
and one distal critical region at 6q27 containing two haploinsufficient genes
DLL1
and
TBP
. Deletions involving the
PRKN
gene could associate with early-onset Parkinson disease and autism spectrum disorder; deletions involving the
DLL1
gene correlate with the 6q terminal deletion syndrome.
Conclusion
The genotype–phenotype correlations for putative haploinsufficient genes in deletions of 6q26-q27 provided evidence for precise diagnostic interpretation, genetic counseling, and clinical management of patients with a deletion of 6q26-q27.
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Xiao G, Qiu X, Zhou Y, Tan G, Shen Y. Prenatal diagnosis of a 4.5-Mb deletion at chromosome 4q35.1q35.2: Case report and literature review. Mol Cytogenet 2021; 14:53. [PMID: 34794455 PMCID: PMC8600819 DOI: 10.1186/s13039-021-00573-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023] Open
Abstract
Objective We present a genetic analysis of an asymptomatic family with a 4q terminal deletion; we also review other similar published studies and discuss the genotype–phenotype correlation. Methods A karyotype analysis was performed on the amniotic fluid cells of a woman at 24 weeks of pregnancy and peripheral blood lymphocytes from both parents and their older son with the conventional G-banding technique. Chromosomal microarray analysis (CMA) testing was carried out for both parents and the fetus to analyze copy number variation (CNV) in the whole genome. Results The results showed no abnormalities in the karyotypes of the father and older son, and the karyotypes of the mother and fetus were 46,XX,del(4)(q35.1) and 46,XY,del(4)(q35.1), respectively. CMA results showed a partial deletion at the 4q terminus in both the fetus and mother. The deletion region of the fetus was arr[GRCh37] 4q35.1q35.2(186,431,008_190,957,460) × 1; the loss size of the CNV was approximately 4.5 Mb and involved 14 protein-coding genes, namely, CYP4V2, F11, FAM149A, FAT1, FRG1, FRG2, KLKB1, MTNR1A, PDLIM3, SORBS2, TLR3, TRIML1, TRIML2, and ZFP42. No variation on chromosome 4 was detected in the father’s CMA results. Conclusion Deletion of the 4q subtelomeric region is a familial variation. The arr[GRCh37] 4q35.1q35.2(186,431,008_190,957,460) region single-copy deletion did not cause obvious congenital defects or mental retardation. The application of high-resolution genetic testing technology combined with the analysis of public genetic database information can more clearly elucidate the genotype–phenotype correlation of the disease and provide support for both prenatal and postnatal genetic counseling.
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Affiliation(s)
- Gefei Xiao
- Department of Clinical Laboratory (Institute of Medical Genetics), Zhuhai Center for Maternal and Child Healthcare, Zhuhai, China
| | - Xianrong Qiu
- Department of Clinical Laboratory (Institute of Medical Genetics), Zhuhai Center for Maternal and Child Healthcare, Zhuhai, China
| | - Yuqiu Zhou
- Department of Clinical Laboratory (Institute of Medical Genetics), Zhuhai Center for Maternal and Child Healthcare, Zhuhai, China
| | - Gongjun Tan
- Department of Clinical Laboratory (Institute of Medical Genetics), Zhuhai Center for Maternal and Child Healthcare, Zhuhai, China.
| | - Yao Shen
- Department of Clinical Laboratory, Zhuhai Hospital of Guangdong Province Traditional Chinese Medicine, Zhuhai, China.
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Meza-Espinoza JP, Contreras-Gutiérrez JA, Arámbula-Meraz E, González-García JR, Domínguez-Quezada MG, García-Magallanes N, Madueña-Molina J, Benítez-Pascual J, Partida-Pérez M, Picos-Cárdenas VJ. Cytogenomic characterization of a de novo 4q34.1 deletion in a girl with mild dysmorphic features and a coagulation disorder. Mol Cytogenet 2021; 14:43. [PMID: 34481514 PMCID: PMC8418750 DOI: 10.1186/s13039-021-00564-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/07/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND 4q deletion syndrome is a rare chromosomal disorder that mostly arises de novo. The syndrome is characterized by craniofacial dysmorphism, digital abnormalities, skeletal alterations, heart malformations, developmental delay, growth retardation, Pierre Robin sequence, autistic spectrum and attention deficit-hyperactivity disorder, although not every patient shows the same features. Array comparative genomic hybridization (aCGH) use improves the detection of tiny chromosomal deletions and allows for a better understanding of genotype-phenotype correlations in affected patients. We report the case of a 6-year-old female patient showing mild dysmorphic features, mild mental disabilities and a coagulation disorder as a consequence of a de novo del(4)(q34.1) characterized by aCGH. CASE PRESENTATION A 6-year-old female patient exhibited special craniofacial features, such as backward-rotated ears, upslanted palpebral fissures, broad nasal bridges, anteverted nares, broad nasal alae, smooth philtrums, smooth nasolabial folds, thin lips, horizontal labial commissures, and retrognathia. In the oral cavity, maxillary deformation, a high arched palate, agenesis of both mandibular canines and fusion of two mandibular incisors were observed. She also displayed bilateral implantation of the proximal thumbs, widely spaced nipples, dorsal kyphosis, hyperlordosis, and clitoral hypertrophy. In addition, the patient presented with coagulopathy, psychomotor delay, attention deficit-hyperactivity disorder, and mild mental disability. A chromosomal study showed the karyotype 46,XX,del(4)(q34.1), while an aCGH analysis revealed an 18.9 Mb deletion of a chromosome 4q subtelomeric region spanning 93 known genes. CONCLUSION The clinical manifestations of this patient were similar to those reported in other individuals with 4q deletion syndrome. Although most of the patients with a 4q34 terminal deletion share similarities, variations in phenotype are also common. In general, clinical effects of chromosomal deletion syndromes depend on the length of the deleted chromosomal segment and, consequently, on the number of lost genes; however, in all of these syndromes, there is no simple correlation between the phenotype and the chromosomal region involved, particularly in cases of 4q deletion.
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Affiliation(s)
- Juan Pablo Meza-Espinoza
- Facultad de Medicina e Ingeniería en Sistemas Computacionales de Matamoros, Universidad Autónoma de Tamaulipas, Matamoros, Tamps., Mexico
| | | | - Eliakym Arámbula-Meraz
- Laboratorio de Genética y Biología Molecular, Posgrado en Ciencias Biomédicas, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sin., Mexico
| | - Juan Ramón González-García
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Ma Guadalupe Domínguez-Quezada
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Noemí García-Magallanes
- Laboratorio de Biomedicina y Biología Molecular, Unidad Académica de Ingeniería en Biotecnología, Universidad Politécnica de Sinaloa, Mazatlán, Sin., Mexico
| | | | | | - Miriam Partida-Pérez
- Departamento de Ciencias Médicas, Centro Universitario de La Costa (CUCosta), Universidad de Guadalajara, Puerto Vallarta, Jalisco, México
| | - Verónica Judith Picos-Cárdenas
- Laboratorio de Genética, Facultad de Medicina, Universidad Autónoma de Sinaloa, Culiacán, Sin., Mexico.
- Servicio de Medicina Genética, Hospital General de Culiacán, Culiacán, Sin., Mexico.
- Núcleo Académico Básico del Programa de Posgrado de la Facultad de Ciencias de la Nutrición y Gastronomía, Universidad Autónoma de Sinaloa, Culiacán, Sin., Mexico.
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Karaman Mercan T, Altiok Clark O, Erkal O, Nur B, Mihci E, Karaman B, Senol AU, Berker Karauzum S. Coexistence of a Homozygous Chromosome 4q35.2 Deletion and Hidden IQSEC2 Pathogenic Variant in a Child with Intellectual Disability. Cytogenet Genome Res 2021; 161:153-159. [PMID: 34229322 DOI: 10.1159/000515368] [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: 09/24/2019] [Accepted: 02/22/2021] [Indexed: 11/19/2022] Open
Abstract
Terminal deletions in the long arm of chromosome 4 are an uncommon event, with a worldwide incidence of approximately 0.001%. The majority of these deletions occur de novo. Terminal deletion cases are usually accompanied by clinical findings that include facial and cardiac anomalies, as well as intellectual disability. In this study, we describe the case of a 2-year-old girl, the fourth child born to consanguineous parents. While her karyotype was normal, a homozygous deletion was identified in the chromosome 4q35.2 region by subtelomeric FISH. A heterozygous deletion of the chromosome 4q35.2 region was observed in both parents. According to the literature, this is the first report of a case that has inherited a homozygous deletion of chromosome 4qter from carrier parents. Subsequent array-CGH analyses were performed on both the case and her parents. Whole-exome sequencing was also carried out to determine potential variants. We detected a NM_001111125.3:c.2329G>T (p.Glu777Ter) nonsense variant of the IQSEC2 gene in the girl, a variant that is related to X-linked intellectual disability.
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Affiliation(s)
- Tuğba Karaman Mercan
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Ozden Altiok Clark
- Department of Medical Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Ozgur Erkal
- Department of Medical Genetics, Antalya Training and Research Hospital, Antalya, Turkey
| | - Banu Nur
- Department of Pediatric Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Ercan Mihci
- Department of Pediatric Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Birsen Karaman
- Department of Medical Genetics, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Abdullah Utku Senol
- Department of Radiodiagnostics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Sibel Berker Karauzum
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
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Meza-Espinoza JP, Sáinz González E, León-León CJN, Arámbula-Meraz E, Contreras-Gutiérrez JA, García-Magallanes N, Madueña-Molina J, Luque-Ortega F, Cervín-Serrano S, Picos-Cárdenas VJ. Report of trisomy 2q34-qter and monosomy 4q35.2-qter in a child with mild dysmorphic syndrome and karyotype 46,XY,der(4)t(2;4)(q34;q35.2)pat. Mol Cytogenet 2020; 13:17. [PMID: 32467733 PMCID: PMC7236877 DOI: 10.1186/s13039-020-00484-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 03/27/2020] [Indexed: 11/10/2022] Open
Abstract
Background Concomitant trisomy 2q3 and monosomy 4q3 have been rarely reported. Pure trisomy 2q3 has been associated with microcephaly, hypertelorism, low-set ears, micrognathia, visceral abnormalities, and growth retardation. Monosomy 4q3 includes a wide variety of dysmorphic features such an abnormal skull shape, hypertelorism, Pierre Robin sequence, short nose with abnormal bridge, fifth finger clinodactyly, congenital heart, and genitourinary defects, in addition to intellectual disability, developmental delay, and hypotonia, but more distal deletions involving 4q34-qter may result in milder phenotypes. Here, we present a child with a mild dysmorphic syndrome, resulted of a duplication 2q34-qter and a deletion 4q35.2-qter inherited of his father. Case presentation We report a child, who at birth presented hypotonia, dysmorphism, and bilateral cryptorchidism. At 2 years and 9 month of age he showed brachycephaly, narrow forehead, bilateral frontoparietal hypertrichosis, down slanting palpebral fissures, sparse eyebrows, sparse short eyelashes, hypertelorism, depressed nasal root, broad nasal bridge, bulbous nasal tip, prominent colummela, broad nasal ala, smooth filtrum, high arched palate, thin upper lips, and ears rotated backwards. He also showed telethelia, hypertrichosis from dorsal to the sacral region, hands with clinodactyly and hypoplasia of the terminal phalanx of the fifth finger, and broad thumbs, broad first toes, and right cryptorchidism. A chromosomal study revealed a karyotype 46,XY,der(4)t(2;4)(q34;q35.2), while an array comparative genomic hybridization showed a 31.12 Mb duplication of the chromosome 2q34-q37.3 and a 1.49 Mb deletion in the chromosome 4q35.2. Conclusions To our knowledge, only four families with translocation t(2;4) have been reported, two of them involving t(2q;4q), but the breakpoints involved in our patient have not been previously observed. The genomic imbalance in this patient was a duplication of 318 genes of the region 2q34-q37.3 and a deletion of 7 genes of 4q35.2. We discuss difficulty to assign specific congenital abnormalities to these duplicated/deleted regions and include some cases with terminal deletions of 4q with normal or just mildly detectable phenotypic effects.
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Affiliation(s)
- Juan Pablo Meza-Espinoza
- 1Facultad de Medicina e Ingeniería en Sistemas Computacionales de Matamoros, Universidad Autónoma de Tamaulipas, Matamoros, Tamps., Mexico
| | | | - Christian J N León-León
- 3Unidad Médica Familiar 11, Instituto Mexicano del Seguro Social (IMSS), Villa Juárez, Navolato, Sin., Mexico
| | - Eliakym Arámbula-Meraz
- 4Laboratorio de Genética y Biología Molecular, Posgrado en Ciencias Biomédicas, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sin., Mexico
| | | | - Noemí García-Magallanes
- Laboratorio de Biomedicina y Biología Molecular, Unidad Académica de Ingeniería en Biotecnología, Universidad Politécnica de Sinaloa, Mazatlán, Sin., Mexico
| | | | - Fred Luque-Ortega
- 7Facultad de Odontología, Universidad Autónoma de Sinaloa, Culiacán, Sin., Mexico
| | | | - Verónica Judith Picos-Cárdenas
- Servicio de Medicina Genética, Hospital General de Culiacán, Culiacán, Sin., Mexico.,8Laboratorio de Genética, Facultad de Medicina, Universidad Autónoma de Sinaloa, Culiacán, Sin., Mexico
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Hryshchenko NV, Bychkova GM, Tavokina LV, Brovko AO, Graziano C, Soloviov OO, Hettinger JA, Patsalis PC, Lurie IW, Livshits LA. Unbalanced translocations involving chromosome region 10q25.3q26.3 in patients with intellectual disability and complex phenotypes. Cytogenet Genome Res 2015; 144:169-77. [PMID: 25573336 DOI: 10.1159/000370086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2014] [Indexed: 11/19/2022] Open
Abstract
We describe 2 Ukrainian families with unbalanced reciprocal translocations (RTs) involving the distal part of chromosome 10q. In both families, the fathers were healthy carriers of the RT. Two affected patients from the first family had an ∼2.3-Mb loss at 10q26.3 and an ∼25-Mb gain at 2q35qter, and the patient from the other family had an ∼12.5-Mb loss at 5p15.2pter and an ∼18-Mb gain at 10q25.3q26.3. We assume that intellectual disability (ID) in association with congenital anomalies observed in our patients was the result of the cumulative effect of both gains and losses of the chromosomal regions involved in each translocation. Comparison of the sizes of the deleted and duplicated segments in our families as well as in other published families with translocations affecting the distal part of 10q showed that generally deletions seem to be ∼2 times more harmful than duplications of the same size. The data obtained here may contribute to improve the diagnosis and genetic counseling of families with similar chromosomal imbalances.
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Affiliation(s)
- Nataliya V Hryshchenko
- Human Genomics Department, Institute of Molecular Biology and Genetics, NASU, Kiev, Ukraine
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11
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Chen X, Li H, Mao Y, Xu X, Lv J, Zhou L, Lin X, Tang S. Subtelomeric multiplex ligation-dependent probe amplification as a supplement for rapid prenatal detection of fetal chromosomal aberrations. Mol Cytogenet 2014; 7:96. [PMID: 25506396 PMCID: PMC4265491 DOI: 10.1186/s13039-014-0096-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/18/2022] Open
Abstract
Background Pregnant women with high-risk indications are highly suspected of fetal chromosomal aberrations. To determine whether Multiplex Ligation-dependent Probe Amplification (MLPA) using subtelomeric probe mixes (P036-E2 and P070-B2) is a reliable method for rapid detection of fetal chromosomal aberrations. The subtelomeric MLPA probe mixes were used to evaluate 50 blood samples from healthy individuals. 168 amniocytes and 182 umbilical cord blood samples from high-risk fetuses were analyzed using the same subtelomeric MLPA probe sets. Karyotyping was also performed in all cases of high-risk pregnancies, and single nucleotide polymorphism array analysis was used to confirm submicroscopic and ambiguous results from MLPA/karyotyping. Results Subtelomeric MLPA analysis of normal samples showed normal result in all cases by use of P036-E2 probe mix, while P070-B2 probe mix gave normal results for all but one case. In one normal control case P070-B2 produced a duplicated signal of probe for 13q34. In the high-risk group, totally 44 chromosomal abnormalities were found by karyotyping and MLPA, including 23 aneuploidies and 21 rearrangements or mosaics. MLPA detected all 23 aneuploidies, 12 rearrangements and 1 mosaic. Importantly, MLPA revealed 4 chromosomal translocations, 2 small supernumerary marker chromosomes (sSMCs), and 3 subtelomeric imbalances that were not well characterized or not detectable by karyotyping. However, MLPA showed negetive results for the remaining 8 rearrangements or mosaics, including 3 low mosaic aneuploidies, 1 inherited sSMC, and 4 paracentric inversions. Conclusions Results suggest that combined use of subtelomeric MLPA and karyotyping may be an alternative method for using karyotype analyses alone in rapid detection of aneuploidies, rearrangements, and sSMCs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-014-0096-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiangnan Chen
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Key Laboratory of Medical Genetics, Zhejiang, China
| | - Huanzheng Li
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Yijian Mao
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Xueqin Xu
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Jiaojiao Lv
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Key Laboratory of Medical Genetics, Zhejiang, China
| | - Lili Zhou
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Xiaoling Lin
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Shaohua Tang
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Key Laboratory of Medical Genetics, Zhejiang, China ; Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
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12
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Moghadasi S, van Haeringen A, Langendonck L, Gijsbers ACJ, Ruivenkamp CAL. A terminal 3p26.3 deletion is not associated with dysmorphic features and intellectual disability in a four-generation family. Am J Med Genet A 2014; 164A:2863-8. [PMID: 25123480 DOI: 10.1002/ajmg.a.36700] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 06/20/2014] [Indexed: 11/06/2022]
Abstract
Terminal deletions of the distal part of the short arm of chromosome 3 cause a wide range of phenotypes from normal to dysmorphic including microcephaly, developmental delay and intellectual disability. We studied the clinical consequences of a terminal deletion of the short arm of chromosome 3 in four generations of a family. The index patient is a14-month-old boy with microcephaly, corpus callosum dysgenesis, and minor dysmorphic features. Single Nucleotide Polymorphism (SNP) array analysis detected a duplication on the long arm of chromosome 6. His apparently healthy mother carries the same 6q duplication, but as an unexpected finding a terminal deletion of 2.9 Mb of the short arm of chromosome 3 was observed. Further co-segregation analysis in the family for the chromosome 3 deletion showed that with the exception of the sister of the index who has autism, speech delay, and learning problems, family members in four generations of this family are carrier of this 3p deletion and apparently healthy. To our knowledge, this is the first report of a study of this terminal 3p deletion in four generations. In this report, we review the literature on terminal 3p deletions and discuss the importance of molecular testing and reporting of copy number variants to achieve accurate genetic counseling in prenatal and postnatal screening.
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Affiliation(s)
- Setareh Moghadasi
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
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13
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Vona B, Nanda I, Neuner C, Schröder J, Kalscheuer VM, Shehata-Dieler W, Haaf T. Terminal chromosome 4q deletion syndrome in an infant with hearing impairment and moderate syndromic features: review of literature. BMC MEDICAL GENETICS 2014; 15:72. [PMID: 24962056 PMCID: PMC4077152 DOI: 10.1186/1471-2350-15-72] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/23/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Terminal deletions of chromosome 4q are associated with a broad spectrum of phenotypes including cardiac, craniofacial, digital, and cognitive impairment. The rarity of this syndrome renders genotype-phenotype correlation difficult, which is further complicated by the widely different phenotypes observed in patients sharing similar deletion intervals. CASE PRESENTATION Herein, we describe a boy with congenital hearing impairment and a variety of moderate syndromic features that prompted SNP array analysis disclosing a heterozygous 6.9 Mb deletion in the 4q35.1q35.2 region, which emerged de novo in the maternal germ line. CONCLUSION In addition to the index patient, we review 35 cases from the literature and DECIPHER database to attempt genotype-phenotype correlations for a syndrome with great phenotypic variability. We delineate intervals with recurrent phenotypic overlap, particularly for cleft palate, congenital heart defect, intellectual disability, and autism spectrum disorder. Broad phenotypic presentation of the terminal 4q deletion syndrome is consistent with incomplete penetrance of the individual symptoms.
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Affiliation(s)
| | | | | | | | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074 Würzburg, Germany.
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14
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Chen CP, Lin MH, Chern SR, Chen YT, Wu PS, Kuo YL, Lee MS, Wang W. Directly transmitted 4.5-Mb triplication of 4q12-q13.1: prenatal diagnosis and molecular cytogenetic characterization. Taiwan J Obstet Gynecol 2014; 53:123-5. [PMID: 24767665 DOI: 10.1016/j.tjog.2013.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Ming-Huei Lin
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yu-Ting Chen
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | | | - Yu-Ling Kuo
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Meng-Shan Lee
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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15
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Thevenon J, Callier P, Andrieux J, Delobel B, David A, Sukno S, Minot D, Mosca Anne L, Marle N, Sanlaville D, Bonnet M, Masurel-Paulet A, Levy F, Gaunt L, Farrell S, Le Caignec C, Toutain A, Carmignac V, Mugneret F, Clayton-Smith J, Thauvin-Robinet C, Faivre L. 12p13.33 microdeletion including ELKS/ERC1, a new locus associated with childhood apraxia of speech. Eur J Hum Genet 2013; 21:82-8. [PMID: 22713806 PMCID: PMC3522191 DOI: 10.1038/ejhg.2012.116] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 04/27/2012] [Accepted: 05/01/2012] [Indexed: 11/10/2022] Open
Abstract
Speech sound disorders are heterogeneous conditions, and sporadic and familial cases have been described. However, monogenic inheritance explains only a small proportion of such disorders, in particular in cases with childhood apraxia of speech (CAS). Deletions of <5 Mb involving the 12p13.33 locus is one of the least commonly deleted subtelomeric regions. Only four patients have been reported with such a deletion diagnosed with fluorescence in situ hybridisation telomere analysis or array CGH. To further delineate this rare microdeletional syndrome, a French collaboration together with a search in the Decipher database allowed us to gather nine new patients with a 12p13.33 subtelomeric or interstitial rearrangement identified by array CGH. Speech delay was found in all patients, which could be defined as CAS when patients had been evaluated by a speech therapist (5/9 patients). Intellectual deficiency was found in 5/9 patients only, and often associated with psychiatric manifestations of various severity. Two such deletions were inherited from an apparently healthy parent, but reevaluation revealed abnormal speech production at least in childhood, suggesting variable expressivity. The ELKS/ERC1 gene, which encodes for a synaptic factor, is found in the smallest region of overlap. These results reinforce the hypothesis that deletions of the 12p13.33 locus may be responsible for variable phenotypes including CAS associated with neurobehavioural troubles and that the presence of CAS justifies a genetic work-up.
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Affiliation(s)
- Julien Thevenon
- Centre de Génétique et Centre de Référence «Anomalies du Développement et Syndromes Malformatifs», Hôpital d'Enfants, CHU Dijon, Dijon, France
| | | | - Joris Andrieux
- Cytogénétique, Hôpital Jeanne de Flandre, CHRU de Lille, Lille, France
| | - Bruno Delobel
- Centre de Cytogénétique Chromosomique, Hôpital Saint Vincent de Paul, Groupe Hospitalier de l'Institut Catholique Lillois, Faculté Libre de Médecine, Lille, France
| | - Albert David
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Sylvie Sukno
- Service de Neuropédiatrie, Hôpital Saint Vincent de Paul, Groupe Hospitalier de l'Institut Catholique Lillois, Faculté Libre de Médecine, Lille, France
| | - Delphine Minot
- Centre de Génétique et Centre de Référence «Anomalies du Développement et Syndromes Malformatifs», Hôpital d'Enfants, CHU Dijon, Dijon, France
| | | | | | - Damien Sanlaville
- Laboratoire de Cytogénétique, CBPE, Hospices Civils de Lyon, Bron, France
| | - Marlène Bonnet
- Centre de Référence des Troubles du Langage et des Apprentissages, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Alice Masurel-Paulet
- Centre de Génétique et Centre de Référence «Anomalies du Développement et Syndromes Malformatifs», Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Fabienne Levy
- Centre de Référence des Troubles du Langage et des Apprentissages, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Lorraine Gaunt
- Genetic Medicine, Manchester Academic Health Science Centre, University of Manchester, Manchester Biomedical Research Centre, St Mary's Hospital, Manchester, UK
| | - Sandra Farrell
- Genetic Medicine, Credit Valley Hospital, Mississauga, Ontario, Canada
| | - Cédric Le Caignec
- Service de Génétique Médicale, CHU Nantes, Nantes, France
- INSERM, UMR_S915, l'institut du thorax, Nantes, France
| | | | | | | | - Jill Clayton-Smith
- Genetic Medicine, Manchester Academic Health Science Centre, University of Manchester, Manchester Biomedical Research Centre, St Mary's Hospital, Manchester, UK
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence «Anomalies du Développement et Syndromes Malformatifs», Hôpital d'Enfants, CHU Dijon, Dijon, France
- Equipe GAD, Université de Bourgogne, Faculté de Médecine, Dijon, France
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence «Anomalies du Développement et Syndromes Malformatifs», Hôpital d'Enfants, CHU Dijon, Dijon, France
- Equipe GAD, Université de Bourgogne, Faculté de Médecine, Dijon, France
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16
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Müller P, Ramel C, Franke K, Riedel S, Junge A, Reichenbach H. Autoimmunerkrankungen, mentale Retardierung und Dysmorphien. Monatsschr Kinderheilkd 2012. [DOI: 10.1007/s00112-012-2701-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Thierry G, Pichon O, Briand A, Poulain D, Sznajer Y, David A, Le Caignec C. Autosomal insertional translocation mimicking an X-linked mode of inheritance. Eur J Med Genet 2012; 56:46-9. [PMID: 23107885 DOI: 10.1016/j.ejmg.2012.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 10/05/2012] [Indexed: 10/27/2022]
Abstract
Unbalanced insertional translocations are a rare cause of intellectual disability. An unbalanced insertional translocation is a rare chromosomal imbalance, which may result from a balanced insertional translocation present in a phenotypically normal parent. We report here three brothers with intellectual disability, short stature, microcephaly, craniofacial anomalies and small testes. Since their parents and their sister were all phenotypically normal, the pattern of the family suggested an X-linked mode of inheritance. Surprisingly, we identified by array comparative genomic hybridization (aCGH) and fluorescent in situ hybridization (FISH) in the three brothers an 8q22.3q23.2 deletion resulting from a balanced insertional translocation present in their healthy father. The deletion encompassed the ZFPM2 gene known to be involved in gonadal development, which is consistent with the small testes and abnormal endocrine dosages in the affected brothers. The present report also illustrates that parental analyses by aCGH or qPCR methods are not sufficient when a de novo deletion or duplication is identified in an affected child and that FISH analysis should be performed on metaphase spreads in both parents to deliver an accurate genetic counseling.
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Affiliation(s)
- Gaelle Thierry
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
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18
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Cambosu F, Capobianco G, Fogu G, Bandiera P, Pirino A, Moro MA, Sanna R, Soro G, Dessole M, Montella A. Partial trisomy of the long arm of chromosome 1: Prenatal diagnosis, clinical evaluation and cytogenetic findings. Case report and review of the literature. J Obstet Gynaecol Res 2012; 39:592-7. [DOI: 10.1111/j.1447-0756.2012.01986.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Ponnala R, Ranganath P, Dutta UR, Pidugu VK, Dalal AB. Phenotypic and molecular characterization of partial trisomy 2q resulting from insertion-duplication in chromosome 18q: a case report and review of literature. Cytogenet Genome Res 2012; 136:229-34. [PMID: 22398442 DOI: 10.1159/000336974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2012] [Indexed: 11/19/2022] Open
Abstract
Trisomy 2q is a well-documented chromosomal anomaly with considerable variation in the phenotype depending upon the breakpoints and the co-existing chromosomal aberrations. The case of a dysmorphic male infant found to have trisomy of the 2q31.1-q37.3 segment, resulting from insertion-duplication of this segment in chromosome 18q23 is reported here. The rearrangement was resolved in detail by cytogenetic microarray and whole chromosome paint-based fluorescence in situ hybridization studies. There is some overlap of the phenotypic features in the reported patient with those described in previously reported cases with partial trisomy 2q. A detailed review of the available literature on 2q trisomy has also been presented and delineation of the phenotypic characteristics common to all patients with 2q trisomy has been attempted.
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Affiliation(s)
- R Ponnala
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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20
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Coca-Pelaz A, Llorente-Pendás JL, García-Martínez J, Vivanco-Allende B, Balbín M, Suárez C, Hermsen M. Medullary thyroid carcinoma and 2q37 deletion in a patient with nevoid basal cell carcinoma syndrome: clinical description and genetic analysis. Head Neck 2012; 35:E147-52. [PMID: 22319002 DOI: 10.1002/hed.22000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2011] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Nevoid basal cell carcinoma syndrome (NBCCS) is a rare, inheritable, multisystem disorder characterized by numerous basal cell carcinomas (BCCs), maxillary keratocyst, and musculoskeletal malformations. Occasionally, it is associated with malignancies like rhabdomyoma, melanoma, and sinonasal undifferentiated carcinoma, to name a few. METHODS A patient presented with NBCCS with a medullary thyroid carcinoma. Clinical, surgical details, and germline genetic analysis are herein described. RESULTS A 32-year-old woman was referred to our department with suspicion of medullary thyroid carcinoma, which was confirmed by histopathological examination. The patient was diagnosed as also having NBCCS. Germline mutation analysis indicated wild-type genes PTCH1 and RET. DNA copy number analysis by high resolution microarray comparative genomic hybridization (CGH) revealed a small interstitial loss at chromosomal band 2q37.3. CONCLUSION To our knowledge, this is the first described patient with NBCCS carrying a medullary thyroid carcinoma and a 2q37 deletion, which confirms that this syndrome can be associated with many different malignancies.
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Affiliation(s)
- Andrés Coca-Pelaz
- Department of Otolaryngology, Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Spain.
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21
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Rashidi-Nezhad A, Parvaneh N, Farzanfar F, Azimi C, Harewood L, Akrami SM, Reymond A. 2q34-qter duplication and 4q34.2-qter deletion in a patient with developmental delay. Eur J Med Genet 2012; 55:203-10. [PMID: 22370062 DOI: 10.1016/j.ejmg.2012.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 01/30/2012] [Indexed: 11/28/2022]
Abstract
The 2q3 duplication and 4q3 deletion syndromes are two conditions with variable phenotypes including Pierre-Robin sequence (PRS), limb anomalies, congenital heart defects (CHD), developmental delays and intellectual disabilities. We describe a patient born to a mother with a balanced t(2; 4) translocation who combines both a 2q34-qter duplication and a 4q34.2-qter deletion through inheritance of the derivative chromosome 4 (der(4)). He showed developmental delay, growth retardation, hearing problems, minor facial and non-facial anomalies, such as bilateral fifth finger shortness and clinodactyly, but no PRS or CHD. The comparison of his features with those of 46 and 65 published cases of 2q3 duplication and 4q3 deletion, respectively, allows us to further restrict the size of the proposed critical intervals for PRS and CHD on chromosome 4.
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Affiliation(s)
- Ali Rashidi-Nezhad
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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22
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Iourov IY, Vorsanova SG, Yurov YB. Molecular cytogenetics and cytogenomics of brain diseases. Curr Genomics 2011; 9:452-65. [PMID: 19506734 PMCID: PMC2691674 DOI: 10.2174/138920208786241216] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 07/06/2008] [Accepted: 07/09/2008] [Indexed: 01/08/2023] Open
Abstract
Molecular cytogenetics is a promising field of biomedical research that has recently revolutionized our thinking on genome structure and behavior. This is in part due to discoveries of human genomic variations and their contribution to biodiversity and disease. Since these studies were primarily targeted at variation of the genome structure, it appears apposite to cover them by molecular cytogenomics. Human brain diseases, which encompass pathogenic conditions from severe neurodegenerative diseases and major psychiatric disorders to brain tumors, are a heavy burden for the patients and their relatives. It has been suggested that most of them, if not all, are of genetic nature and several recent studies have supported the hypothesis assuming them to be associated with genomic instabilities (i.e. single-gene mutations, gross and subtle chromosome imbalances, aneuploidy). The present review is focused on the intriguing relationship between genomic instability and human brain diseases. Looking through the data, we were able to conclude that both interindividual and intercellular genomic variations could be pathogenic representing, therefore, a possible mechanism for human brain malfunctioning. Nevertheless, there are still numerous gaps in our knowledge concerning the link between genomic variations and brain diseases, which, hopefully, will be filled by forthcoming studies. In this light, the present review considers perspectives of this dynamically developing field of neurogenetics and genomics.
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Affiliation(s)
- I Y Iourov
- National Research Center of Mental Health, Russian Academy of Medical Sciences
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Gerber J, Neuhann T, Tyshchenko N, Smitka M, Hackmann K. Expanding the clinical and neuroradiological phenotype of 6q27 microdeletion: Olfactory bulb aplasia and anosmia. Am J Med Genet A 2011; 155A:1981-6. [DOI: 10.1002/ajmg.a.34079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Accepted: 04/06/2011] [Indexed: 11/11/2022]
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Carmany EP, Bawle EV. Microduplication of 4p16.3 due to an unbalanced translocation resulting in a mild phenotype. Am J Med Genet A 2011; 155A:819-24. [DOI: 10.1002/ajmg.a.33916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 12/23/2010] [Indexed: 11/08/2022]
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Tenney JR, Hopkin RJ, Schapiro MB. Deletion of 14-3-3{varepsilon} and CRK: a clinical syndrome with macrocephaly, developmental delay, and generalized epilepsy. J Child Neurol 2011; 26:223-7. [PMID: 20833799 DOI: 10.1177/0883073810379638] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Deletions of chromosome 17p13.3 result in neuronal migration defects such as isolated lissencephaly sequence and Miller-Dieker syndrome. LIS1 is the deleted gene within this region and is thought to directly cause isolated lissencephaly sequence and contribute to Miller-Dieker syndrome. Two additional genes (14-3-3ε and CRK) on the telomeric end of chromosome 17p reportedly contribute to the severe phenotype of Miller-Dieker syndrome. We report 2 patients with deletions of chromosome 17p13.3 involving the genes 14-3-3ε and CRK but not LIS1 with previously unreported, identical phenotypes of macrocephaly, small stature, dysmorphic features, generalized epilepsy, developmental delay, and nonspecific white matter changes. The findings in this report suggest that patients who have deletions of 14-3-3ε and/or CRK should be monitored closely for the development of seizures.
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Affiliation(s)
- Jeffrey R Tenney
- Division of Neurology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, and University of Cincinnati College of Medicine, Cincinnati, OH 45229-3039, USA.
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A parallel SNP array study of genomic aberrations associated with mental retardation in patients and general population in Estonia. Eur J Med Genet 2010; 54:136-43. [PMID: 21112420 DOI: 10.1016/j.ejmg.2010.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 11/04/2010] [Indexed: 11/21/2022]
Abstract
The increasing use of whole-genome array screening has revealed the important role of DNA copy-number variations in the pathogenesis of neurodevelopmental disorders and several recurrent genomic disorders have been defined during recent years. However, some variants considered to be pathogenic have also been observed in phenotypically normal individuals. This underlines the importance of further characterization of genomic variants with potentially variable expressivity in both patient and general population cohorts to clarify their phenotypic consequence. In this study whole-genome SNP arrays were used to investigate genomic rearrangements in 77 Estonian families with idiopathic mental retardation. In addition to this family-based approach, phenotype and genotype data from a cohort of 1000 individuals in the general population were used for accurate interpretation of aberrations found in mental retardation patients. Relevant structural aberrations were detected in 18 of the families analyzed (23%). Fifteen of those were in genomic regions where clinical significance has previously been established. In 3 families, 4 novel aberrations associated with intellectual disability were detected in chromosome regions 2p25.1-p24.3, 3p12.1-p11.2, 7p21.2-p21.1 and Xq28. Carriers of imbalances in 15q13.3, 16p11.2 and Xp22.31 were identified among reference individuals, affirming the variable phenotypic consequence of rare variants in some genomic regions considered as pathogenic.
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Vera-Carbonell A, López-Expósito I, Bafalliu JA, Ballesta-Martínez M, Glóver G, Llópis C, Moya-Quiles R, Suela J, Fernández A, Guillén-Navarro E. Molecular characterization of a new patient with a non-recurrent inv dup del 2q and review of the mechanisms for this rearrangement. Am J Med Genet A 2010; 152A:2670-80. [PMID: 20799321 DOI: 10.1002/ajmg.a.33613] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report on newborn baby with microcephaly, facial anomalies, congenital heart defects, hypotonia, wrist contractures, long fingers, adducted thumbs, and club feet. Cytogenetic studies revealed an inverted duplication with terminal deletion (inv dup del) of 2q in the patient and a paternal 2qter deletion polymorphism. Microsatellite markers demonstrated that the inv dup del was maternal in origin and intrachromosomal. Intra or interchromosomal rearrangements may cause this aberration either by a U-type exchange (end-to-end fusion), an unequal crossover between inverted repeats (non-allelic homologous recombination: NAHR), or through breakage-fusion-bridge (BFB) cycles leading to a sister chromatid fusion by non-homologous end joining (NHEJ). A high-resolution oligo array-CGH (244 K) defined the breakpoints and did not detect a single copy region with a size exceeding 12.93 Kb in the fusion site. The size of the duplicated segment was 38.75 Mb, extending from 2q33.1 to 2q37.3 and the size of the terminal deletion was 2.85 Mb in 2q37.3. Our results indicate that the inv dup del (2q) is likely a non-recurrent chromosomal rearrangement generated by a NHEJ mechanism. The major clinical characteristics associated with this 2q rearrangement overlap with those commonly found in patients with 2q duplication reported in the literature.
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Affiliation(s)
- Ascensión Vera-Carbonell
- Sección de Citogenética, Centro de Bioquímica y Genética Clínica, Hospital U. Virgen de la Arrixaca, Murcia, Spain
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Christofolini DM, de Paula Ramos MA, Kulikowski LD, da Silva Bellucco FT, Belangero SIN, Brunoni D, Melaragno MI. Subtelomeric rearrangements and copy number variations in people with intellectual disabilities. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2010; 54:938-942. [PMID: 20807304 DOI: 10.1111/j.1365-2788.2010.01325.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND The most prevalent type of structural variation in the human genome is represented by copy number variations that can affect transcription levels, sequence, structure and function of genes. METHOD In the present study, we used the multiplex ligation-dependent probe amplification (MLPA) technique and quantitative PCR for the detection of copy number variation in 132 intellectually disabled male patients with normal karyotypes and negative fragile-X-testing. RESULTS Ten of these patients (7.6%) showed copy number variation in the subtelomeric regions, including deletions and duplications. DISCUSSION Duplications of the SECTM1 gene, located at 17q25.3, and of the FLJ22115 gene, located at 20p13, could be associated with phenotype alterations. This study highlights the relevance in the aetiology of intellectual disability of subtelomeric rearrangements that can be screened by MLPA and other molecular techniques.
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Affiliation(s)
- D M Christofolini
- Morphology and Genetics Department, Universidade Federal de São Paulo, São Paulo, SP, Brazil
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Lenzini E, Drigo P, Redaelli S, Mammi I, Rosa-Rizzotto M, Dalprà L. Familial subtelomeric rearrangement of chromosomes 19 and 20: a new contribution to partial distal 19q trisomy. Genet Test Mol Biomarkers 2010; 14:695-701. [PMID: 20854099 DOI: 10.1089/gtmb.2010.0079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The role of cryptic translocations in human syndromes is a matter of fact, though this phenomenon is apparently rare. Apart from episodic case reports due to the increasing application of new molecular cytogenetic techniques, no data on its frequency in the general population are currently available. Rearrangements due to the unbalanced segregation of cryptic translocations are found in many anomalies responsible for different clinical pictures. In nearly 50% of cases, subtelomeric abnormalities are inherited from a parent carrying a balanced cryptic chromosome rearrangement. To date, very few cases of partial trisomies of 19q have been reported, with different breakpoints. Involvement of the distal region 19q is even more rare, and the delineation of its main clinical characteristics is still vague and awaiting better definition. We report two new cases of partial 19q13.42-qter trisomy associated with a partial 20p13-pter monosomy in a family found to have the cryptic translocation t(19;20)(q13.42;p13). We investigated a 5-year-old boy and his 49-year-old paternal uncle, and both had a similar, previously unrecognized mental retardation pattern, associated with the same subtelomeric rearrangement.
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Hila L, Tébourbi H, Abeid L, Rejeb I, Chaabouni H. Subtelomeric microduplications in three sisters with moderate mental retardation. Biochem Genet 2010; 48:909-14. [PMID: 20811773 DOI: 10.1007/s10528-010-9371-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 04/26/2010] [Indexed: 11/26/2022]
Abstract
Copy number changes of subtelomeric regions are a common cause of mental retardation, occurring in approximately 5% of mentally retarded patients. New molecular techniques allow the identification of subtelomeric microduplications. We report a Tunisian family of three sisters with moderate mental retardation, facial dysmorphism, cardiopathy, and bilateral clinodactyly of the third and fourth toes, explored by MLPA, showing the same associated microduplications, 15q and Xq, without a concurrent deletion.
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Affiliation(s)
- Lamia Hila
- Faculté de Médecine de Tunis, Laboratoire de Génétique Humaine, Tunisia.
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Distal trisomy 10q syndrome: phenotypic features in a child with inverted duplicated 10q25.1–q26.3. Clin Dysmorphol 2010; 19:140-145. [DOI: 10.1097/mcd.0b013e3283377915] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Submicroscopic subtelomeric aberrations in Chinese patients with unexplained developmental delay/mental retardation. BMC MEDICAL GENETICS 2010; 11:72. [PMID: 20459802 PMCID: PMC2892449 DOI: 10.1186/1471-2350-11-72] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Accepted: 05/11/2010] [Indexed: 01/16/2023]
Abstract
BACKGROUND Subtelomeric imbalance is widely accepted as related to developmental delay/mental retardation (DD/MR). Fine mapping of aberrations in gene-enriched subtelomeric regions provides essential clues for localizing critical regions, and provides a strategy for identifying new candidate genes. To date, no large-scale study has been conducted on subtelomeric aberrations in DD/MR patients in mainland China. METHODS This study included 451 Chinese children with moderate to severe clinically unexplained DD/MR. The subtelomere-MLPA (multiplex ligation dependent probe amplification) and Affymetrix human SNP array 6.0 were used to determine the subtelomeric copy number variations. The exact size and the breakpoint of each identified aberration were well defined. RESULTS The submicroscopic subtelomeric aberrations were identified in 23 patients, with a detection rate of 5.1%. 16 patients had simple deletions, 2 had simple duplications and 5 with both deletions and duplications. The deletions involved 14 different subtelomeric regions (1p, 2p, 4p, 6p, 7p, 7q, 8p, 9p, 10p, 11q, 14q, 15q, 16p and 22q), and duplications involved 7 subtelomeric regions (3q, 4p, 6q, 7p, 8p, 12p and 22q). Of all the subtelomeric aberrations found in Chinese subjects, the most common was 4p16.3 deletion. The sizes of the deletions varied from 0.6 Mb to 12 Mb, with 5-143 genes inside. Duplicated regions were 0.26 Mb to 11 Mb, with 6-202 genes inside. In this study, four deleted subtelomeric regions and one duplicated region were smaller than any other previously reported, specifically the deletions in 11q25, 8p23.3, 7q36.3, 14q32.33, and the duplication in 22q13. Candidate genes inside each region were proposed. CONCLUSIONS Submicroscopic subtelomeric aberrations were detected in 5.1% of Chinese children with clinically unexplained DD/MR. Four deleted subtelomeric regions and one duplicated region found in this study were smaller than any previously reported, which will be helpful for further defining the candidate dosage sensitive gene associated with DD/MR.
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Rossi MR, DiMaio MS, Xiang B, Lu K, Kaymakcalan H, Seashore M, Mahoney MJ, Li P. Clinical and genomic characterization of distal duplications and deletions of chromosome 4q: study of two cases and review of the literature. Am J Med Genet A 2010; 149A:2788-94. [PMID: 19921640 DOI: 10.1002/ajmg.a.33088] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Variable clinical presentations of patients with chromosomally detected deletions in the distal long arm (q) of chromosome 4 have been reported. The lack of molecular characterization of the deletion sizes and deleted genes hinders further genotype-phenotype correlation. Using a validated oligonucleotide array comparative genomic hybridization (oaCGH) analysis, we examined two patients with apparent chromosomal deletions in the distal 4q region. In the first, oaCGH identified a 2.441 megabase (Mb) duplication and a 12.651 Mb deletion at 4q34.1 in a pregnant female who transmitted this aberration to her son. This mother has only learning disabilities while her son had both renal and cardiac anomalies in the newborn period. Unrecognized paternal genetic factors may contribute to the variable expression. The second patient is a 17-year-old female with a history of Pierre Robin sequence, cardiac abnormalities and learning disabilities. She was diagnosed prenatally with a de novo 4q deletion, and oaCGH defined a 16.435 Mb deletion of 4q34.1-4q35.2. Phenotypic comparison and subtractive genomic mapping between these two cases suggested a 4 Mb region possibly harboring a candidate gene for Pierre Robin sequence. Our cases and review of reported cases with genomic findings indicated the presence of familial variants with variable expressivity as well as de novo or inherited pathogenic simple deletion, duplication and complex deletion and duplication in the distal 4q region.
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Affiliation(s)
- Michael R Rossi
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
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Elbracht M, Roos A, Schönherr N, Busse S, Damen R, Zerres K, Rudnik-Schöneborn S, Schüler HM. Pure distal trisomy 2q: A rare chromosomal abnormality with recognizable phenotype. Am J Med Genet A 2009; 149A:2547-50. [DOI: 10.1002/ajmg.a.33086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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de Ravel T, Balikova I, Van Driessche J, Vermeesch J, Fryns JP. "Opitz C syndrome and pseudohypoaldosteronism" is caused by a chromosome 4q deletion. Am J Med Genet A 2009; 149A:1315-6. [PMID: 19449408 DOI: 10.1002/ajmg.a.32817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Belligni EF, Biamino E, Molinatto C, Messa J, Pierluigi M, Faravelli F, Zuffardi O, Ferrero GB, Silengo MC. Subtelomeric FISH analysis in 76 patients with syndromic developmental delay/intellectual disability. Ital J Pediatr 2009; 35:9. [PMID: 19490664 PMCID: PMC2687548 DOI: 10.1186/1824-7288-35-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 04/27/2009] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Intellectual disability affects approximately 1 to 3% of the general population. The etiology is still poorly understood and it is estimated that one-half of the cases are due to genetic factors. Cryptic subtelomeric aberrations have been found in roughly 5 to 7% of all cases. METHODS We performed a subtelomeric FISH analysis on 76 unrelated children with normal standard karyotype ascertained by developmental delay or intellectual disability, associated with congenital malformations, and/or facial dysmorphisms. RESULTS Ten cryptic chromosomal anomalies have been identified in the whole cohort (13,16%), 8 in the group of patients characterized by developmental delay or intellectual disability associated with congenital malformations and facial dysmorphisms, 2 in patients with developmental delay or intellectual disability and facial dysmorphisms only. CONCLUSION We demonstrate that a careful clinical examination is a very useful tool for pre-selection of patients for genomic analysis, clearly enhancing the chromosomal anomaly detection rate. Clinical features of most of these patients are consistent with the corresponding emerging chromosome phenotypes, pointing out these new clinical syndromes associated with specific genomic imbalances.
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Affiliation(s)
- Elga F Belligni
- Dipartimento di Scienze Pediatriche, University of Torino, Torino, Italy
| | - Elisa Biamino
- Dipartimento di Scienze Pediatriche, University of Torino, Torino, Italy
| | - Cristina Molinatto
- Dipartimento di Scienze Pediatriche, University of Torino, Torino, Italy
| | - Jole Messa
- Dipartimento di Biologia Generale e Genetica Medica, University of Pavia, Pavia, Italy
| | | | | | - Orsetta Zuffardi
- Dipartimento di Biologia Generale e Genetica Medica, University of Pavia, Pavia, Italy
| | - Giovanni B Ferrero
- Dipartimento di Scienze Pediatriche, University of Torino, Torino, Italy
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Nine patients with a microdeletion 15q11.2 between breakpoints 1 and 2 of the Prader-Willi critical region, possibly associated with behavioural disturbances. Eur J Med Genet 2009; 52:108-15. [PMID: 19328872 DOI: 10.1016/j.ejmg.2009.03.010] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Accepted: 03/18/2009] [Indexed: 11/21/2022]
Abstract
Behavioural differences have been described in patients with type I deletions (between breakpoints 1 and 3 (BP1-BP3)) or type II deletions (between breakpoints 2 and 3) of the 15q11.2 Prader-Willi/Angelman region. The larger type I deletions appear to coincide with more severe behavioural problems (autism, ADHD, obsessive-compulsive disorder). The non-imprinted chromosomal segment between breakpoints 1 and 2 involves four highly conserved genes, TUBGCP5, NIPA1, NIPA2, and CYFIP1; the latter three are widely expressed in the central nervous system, while TUBGCP5 is expressed in the subthalamic nuclei. These genes might explain the more severe behavioural problems seen in type I deletions. We describe nine cases with a microdeletion at 15q11.2 between BP1-BP2, thus having a haploinsufficiency for TUBGCP5, NIPA1, NIPA2, and CYFIP1 without Prader-Willi/Angelman syndrome. The clinical significance of a pure BP1-BP2 microdeletion has been debated, however, our patients shared several clinical features, including delayed motor and speech development, dysmorphisms and behavioural problems (ADHD, autism, obsessive-compulsive behaviour). Although the deletion often appeared to be inherited from a normal or mildly affected parent, it was de novo in two cases and we did not find it in 350 healthy unrelated controls. Our results suggest a pathogenic nature for the BP1-BP2 microdeletion and, although there obviously is an incomplete penetrance, they support the existence of a novel microdeletion syndrome in 15q11.2.
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Auber B, Bruemmer V, Zoll B, Burfeind P, Boehm D, Liehr T, Brockmann K, Wilichowski E, Argyriou L, Bartels I. Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation. Mol Cytogenet 2009; 2:10. [PMID: 19284615 PMCID: PMC2660352 DOI: 10.1186/1755-8166-2-10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 03/12/2009] [Indexed: 01/04/2023] Open
Abstract
Background Submicroscopic imbalances in the subtelomeric regions of the chromosomes are considered to play an important role in the aetiology of mental retardation (MR). The aim of the study was to evaluate a quantitative PCR (qPCR) protocol established by Boehm et al. (2004) in the clinical routine of subtelomeric testing. Results 296 patients with MR and a normal karyotype (500–550 bands) were screened for subtelomeric imbalances by using qPCR combined with SYBR green detection. In total, 17 patients (5.8%) with 20 subtelomeric imbalances were identified. Six of the aberrations (2%) were classified as causative for the symptoms, because they occurred either de novo in the patients (5 cases) or the aberration were be detected in the patient and an equally affected parent (1 case). The extent of the deletions ranged from 1.8 to approximately 10 Mb, duplications were 1.8 to approximately 5 Mb in size. In 6 patients, the copy number variations (CNVs) were rated as benign polymorphisms, and the clinical relevance of these CNVs remains unclear in 5 patients (1.7%). Therefore, the overall frequency of clinically relevant imbalances ranges between 2% and 3.7% in our cohort. Conclusion This study illustrates that the qPCR/SYBR green technique represents a rapid and versatile method for the detection of subtelomeric imbalances and the option to map the breakpoint. Thus, this technique is highly suitable for genotype/phenotype studies in patients with MR/developmental delay and/or congenital defects.
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Affiliation(s)
- Bernd Auber
- Institute of Human Genetics, Georg August University, Göttingen, Germany.
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de Ravel TJ, Balikova I, Thiry P, Vermeesch JR, Frijns JP. Another patient with a de novo deletion further delineates the 2q33.1 microdeletion syndrome. Eur J Med Genet 2009; 52:120-2. [PMID: 19284984 DOI: 10.1016/j.ejmg.2009.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Accepted: 01/09/2009] [Indexed: 11/26/2022]
Abstract
A male patient, who had intra-uterine growth retardation, a low birth weight and hypotonia due to a chromosome 2q33.1 deletion, is described. At the age of 20 years, he displays short stature, microcephaly, a high forehead, microstomia, large teeth and is hypertonic. He is severely mentally retarded, has not developed speech, is hyperactive, anxious and at times aggressive. Full tiling array showed a de novo 14 Mb deletion at chromosome region 2q32.3q33.2, further delineating the 2q33.1 microdeletion syndrome.
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Affiliation(s)
- Thomy J de Ravel
- University Hospitals of Leuven, Center for Human Genetics, Herestraat 49, B-3000 Leuven, Belgium.
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Balikova I, Vermeesch JR, Fryns JP, Van Esch H. Bronchiectasis and immune deficiency in an adult patient with deletion 2q37 due to an unbalanced translocation t(2;10). Eur J Med Genet 2009; 52:260-1. [PMID: 19272308 DOI: 10.1016/j.ejmg.2009.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 01/05/2009] [Indexed: 10/21/2022]
Abstract
We describe a female patient with der(2) t(2;10)(q37;q26). She presented with congenital malformations typical of a terminal 2q deletion, associated with immune deficiency leading to bronchiectasis.
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Affiliation(s)
- Irina Balikova
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, B-3000 Leuven, Belgium
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South ST, Hannes F, Fisch GS, Vermeesch JR, Zollino M. Pathogenic significance of deletions distal to the currently described Wolf-Hirschhorn syndrome critical regions on 4p16.3. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2008; 148C:270-4. [DOI: 10.1002/ajmg.c.30188] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Göhring I, Blümlein HM, Hoyer J, Ekici AB, Trautmann U, Rauch A. 6.7 Mb interstitial duplication in chromosome band 11q24.2q25 associated with infertility, minor dysmorphic features and normal psychomotor development. Eur J Med Genet 2008; 51:666-71. [DOI: 10.1016/j.ejmg.2008.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 07/24/2008] [Indexed: 12/24/2022]
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Engbers H, van der Smagt JJ, van 't Slot R, Vermeesch JR, Hochstenbach R, Poot M. Wolf-Hirschhorn syndrome facial dysmorphic features in a patient with a terminal 4p16.3 deletion telomeric to the WHSCR and WHSCR 2 regions. Eur J Hum Genet 2008; 17:129-32. [PMID: 18830230 DOI: 10.1038/ejhg.2008.168] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We report on a patient with developmental delay and several facial characteristics reminiscent of Wolf-Hirschhorn syndrome, who carries a terminal 4p16.3 deletion of minimally 1.691 Mb and maximally 1.698 Mb. This deletion contains the FGFRL1 gene, but does not include the WHSC1 gene. Given its expression pattern and its involvement in bone and cartilage formation during embryonic development, the FGFRL1 gene represents a plausible candidate gene for part of the facial characteristics of Wolf-Hirshhorn syndrome in 4p16.3 deletion patients.
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Affiliation(s)
- Hannelie Engbers
- Department of Medical Genetics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.
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Piccione M, Antona V, Piro E, Cavani S, Malacarne M, Pierluigi M, Corsello G. 10qter deletion: A new case. Am J Med Genet A 2008; 146A:2435-8. [DOI: 10.1002/ajmg.a.32467] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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45
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Gouas L, Goumy C, Véronèse L, Tchirkov A, Vago P. Gene dosage methods as diagnostic tools for the identification of chromosome abnormalities. ACTA ACUST UNITED AC 2008; 56:345-53. [DOI: 10.1016/j.patbio.2008.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 03/14/2008] [Indexed: 10/22/2022]
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46
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Rodríguez L, Niebuhr E, García A, Martínez-Fernández ML, Peña Segura JL. Be careful with familial unbalanced chromosome abnormalities! Am J Med Genet A 2008; 146A:2005-7. [PMID: 18627044 DOI: 10.1002/ajmg.a.32383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- L Rodríguez
- Estudio Colaborativo Español de Malformaciones Congénitas del Centro de Investigación sobre Anomalías Congénitas, Instituto de Salud Carlos III, Ministerio de Sanidad y Consumo, Madrid, Spain.
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47
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Queralt R, Madrigal I, Vallecillos MA, Morales C, Ballescá JL, Oliva R, Soler A, Sánchez A, Margarit E. Atypical XX male with the SRY gene located at the long arm of chromosome 1 and a 1qter microdeletion. Am J Med Genet A 2008; 146A:1335-40. [PMID: 18412126 DOI: 10.1002/ajmg.a.32284] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Male individuals with a 46,XX karyotype have been designated as XX males. In 80% of the cases, the presence of Yp sequences, including the male sex-determining gene, SRY, has been demonstrated by molecular and/or fluorescence in situ hybridization (FISH) analyses. In most cases, Yp sequences are located on the short arm of the X chromosome, resulting from unequal recombination between Yp and Xp during paternal meiosis. Much less frequent in XX males is the localization of the SRY gene to an autosome. Here we report on the genetic investigation of an atypical XX male in which the SRY gene was located at the end of the long arm of chromosome 1. The patient, with a normal male phenotype, was referred for azoospermia. Conventional cytogenetic analysis showed a 46,XX karyotype. Molecular-cytogenetics (FISH) and molecular (PCR and MLPA) studies identified not only Yp-specific sequences located on the distal long arm of chromosome 1 but also the deletion of the subtelomeric 1qter region. A specific phenotype has been reported for a deletion of the 1qter region associated with mental retardation. The molecular investigation of the 1qter region showed that in our patient the microdeletion is more telomeric than in patients reported with mental retardation. To our knowledge, this is the first report of a XX male with the Yp region transferred to the terminal long arm of chromosome 1. This is also the first microdeletion of the subtelomeric 1qter region not associated with mental retardation.
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Affiliation(s)
- Rosa Queralt
- Servei de Bioquímica i Genètica Molecular, Hospital Clínic, Barcelona, Spain
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48
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Isidor B, Winer N, Joubert M, Boisseau P, Le Caignec C, Bocéno M, Fallet C, David A, Rival JM. Inherited 18q23 duplication in a fetus with multiple congenital anomalies. Eur J Med Genet 2008; 51:231-8. [DOI: 10.1016/j.ejmg.2007.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 12/28/2007] [Indexed: 12/08/2022]
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49
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Eggermann K, Schönherr N, Ranke MB, Wollmann HA, Binder G, Eggermann T. Search for Subtelomeric Imbalances by Multiplex Ligation-Dependent Probe Amplification in Silver–Russell Syndrome. ACTA ACUST UNITED AC 2008; 12:111-3. [DOI: 10.1089/gte.2007.0075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | | | | | | | - Gerhard Binder
- Children's Hospital, University of Tübingen, Tübingen, Germany
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50
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Bonaglia MC, Giorda R, Beri S, Peters GB, Kirk EP, Hung D, Ciccone R, Gottardi G, Zuffardi O. Concurrent transposition of distal 6p and 20q to the 22q telomere: A recurrent benign chromosomal variant. Eur J Med Genet 2008; 51:148-55. [DOI: 10.1016/j.ejmg.2007.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Accepted: 11/23/2007] [Indexed: 12/08/2022]
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