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Hayashi S, Uehara DT, Tanimoto K, Mizuno S, Chinen Y, Fukumura S, Takanashi JI, Osaka H, Okamoto N, Inazawa J. Comprehensive investigation of CASK mutations and other genetic etiologies in 41 patients with intellectual disability and microcephaly with pontine and cerebellar hypoplasia (MICPCH). PLoS One 2017; 12:e0181791. [PMID: 28783747 PMCID: PMC5546575 DOI: 10.1371/journal.pone.0181791] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/09/2017] [Indexed: 01/10/2023] Open
Abstract
The CASK gene (Xp11.4) is highly expressed in the mammalian nervous system and plays several roles in neural development and synaptic function. Loss-of-function mutations of CASK are associated with intellectual disability and microcephaly with pontine and cerebellar hypoplasia (MICPCH), especially in females. Here, we present a comprehensive investigation of 41 MICPCH patients, analyzed by mutational search of CASK and screening of candidate genes using an SNP array, targeted resequencing and whole-exome sequencing (WES). In total, we identified causative or candidate genomic aberrations in 37 of the 41 cases (90.2%). CASK aberrations including a rare mosaic mutation in a male patient, were found in 32 cases, and a mutation in ITPR1, another known gene in which mutations are causative for MICPCH, was found in one case. We also found aberrations involving genes other than CASK, such as HDAC2, MARCKS, and possibly HS3ST5, which may be associated with MICPCH. Moreover, the targeted resequencing screening detected heterozygous variants in RELN in two cases, of uncertain pathogenicity, and WES analysis suggested that concurrent mutations of both DYNC1H1 and DCTN1 in one case could lead to MICPCH. Our results not only identified the etiology of MICPCH in nearly all the investigated patients but also suggest that MICPCH is a genetically heterogeneous condition, in which CASK inactivating mutations appear to account for the majority of cases.
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Affiliation(s)
- Shin Hayashi
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, United States of America
- * E-mail: (SH); (JI)
| | - Daniela Tiaki Uehara
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kousuke Tanimoto
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Genome Laboratory, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Kasugai, Japan
| | - Yasutsugu Chinen
- Department of Pediatrics, University of the Ryukyus School of Medicine, Nishihara, Japan
| | - Shinobu Fukumura
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Jun-ichi Takanashi
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, Yachiyo, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical School, Tochigi, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
- * E-mail: (SH); (JI)
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Associations between the clinical findings of cases having submicroscopic chromosomal imbalances at chromosomal breakpoints of apparently balanced structural rearrangements. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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3
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Morishita M, Muramatsu T, Suto Y, Hirai M, Konishi T, Hayashi S, Shigemizu D, Tsunoda T, Moriyama K, Inazawa J. Chromothripsis-like chromosomal rearrangements induced by ionizing radiation using proton microbeam irradiation system. Oncotarget 2016; 7:10182-92. [PMID: 26862731 PMCID: PMC4891112 DOI: 10.18632/oncotarget.7186] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/24/2016] [Indexed: 12/11/2022] Open
Abstract
Chromothripsis is the massive but highly localized chromosomal rearrangement in response to a one-step catastrophic event, rather than an accumulation of a series of subsequent and random alterations. Chromothripsis occurs commonly in various human cancers and is thought to be associated with increased malignancy and carcinogenesis. However, the causes and consequences of chromothripsis remain unclear. Therefore, to identify the mechanism underlying the generation of chromothripsis, we investigated whether chromothripsis could be artificially induced by ionizing radiation. We first elicited DNA double-strand breaks in an oral squamous cell carcinoma cell line HOC313-P and its highly metastatic subline HOC313-LM, using Single Particle Irradiation system to Cell (SPICE), a focused vertical microbeam system designed to irradiate a spot within the nuclei of adhesive cells, and then established irradiated monoclonal sublines from them, respectively. SNP array analysis detected a number of chromosomal copy number alterations (CNAs) in these sublines, and one HOC313-LM-derived monoclonal subline irradiated with 200 protons by the microbeam displayed multiple CNAs involved locally in chromosome 7. Multi-color FISH showed a complex translocation of chromosome 7 involving chromosomes 11 and 12. Furthermore, whole genome sequencing analysis revealed multiple de novo complex chromosomal rearrangements localized in chromosomes 2, 5, 7, and 20, resembling chromothripsis. These findings suggested that localized ionizing irradiation within the nucleus may induce chromothripsis-like complex chromosomal alterations via local DNA damage in the nucleus.
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Affiliation(s)
- Maki Morishita
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, Japan
| | - Tomoki Muramatsu
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yumiko Suto
- Biodosimetry Research Team, Research Center for Radiation Emergency Medicine, National Institute of Radiological Sciences, Inage-ku, Chiba-shi, Chiba, Japan
| | - Momoki Hirai
- Biodosimetry Research Team, Research Center for Radiation Emergency Medicine, National Institute of Radiological Sciences, Inage-ku, Chiba-shi, Chiba, Japan
| | - Teruaki Konishi
- Research Development and Support Center, National Institute of Radiological Sciences, Inage-ku, Chiba-shi, Chiba, Japan
| | - Shin Hayashi
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Daichi Shigemizu
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Tsurumi, Yokohama, Japan
| | - Tatsuhiko Tsunoda
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Tsurumi, Yokohama, Japan
| | - Keiji Moriyama
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
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Uehara DT, Hayashi S, Okamoto N, Mizuno S, Chinen Y, Kosaki R, Kosho T, Kurosawa K, Matsumoto H, Mitsubuchi H, Numabe H, Saitoh S, Makita Y, Hata A, Imoto I, Inazawa J. SNP array screening of cryptic genomic imbalances in 450 Japanese subjects with intellectual disability and multiple congenital anomalies previously negative for large rearrangements. J Hum Genet 2016; 61:335-43. [PMID: 26740234 DOI: 10.1038/jhg.2015.154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/30/2015] [Accepted: 11/20/2015] [Indexed: 11/09/2022]
Abstract
Intellectual disability (ID) is a heterogeneous condition affecting 2-3% of the population, often associated with multiple congenital anomalies (MCA). The genetic cause remains largely unexplained for most cases. To investigate the causes of ID/MCA of unknown etiology in the Japanese population, 645 subjects have been recruited for the screening of pathogenic copy-number variants (CNVs). Two screenings using bacterial artificial chromosome (BAC) arrays were previously performed, which identified pathogenic CNVs in 133 cases (20.6%; Hayashi et al., J. Hum. Genet., 2011). Here, we present the findings of the third screening using a single-nucleotide polymorphism (SNP) array, performed in 450 negative cases from our previous report. Pathogenic CNVs were found in 22 subjects (4.9%), in which 19 CNVs were located in regions where clinical significance had been previously established. Among the 22 cases, we identified PPFIA2 as a novel candidate gene for ID. Analysis of copy-neutral loss of heterozygosity (CNLOH) detected one case in which the CNLOH regions seem to be significant. The SNP array detected a modest fraction of small causative CNVs, which is explained by the fact that the majority of causative CNVs have larger sizes, and those had been mostly identified in the two previous screenings.
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Affiliation(s)
- Daniela Tiaki Uehara
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shin Hayashi
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Kasugai, Japan
| | - Yasutsugu Chinen
- Department of Pediatrics, Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Hiroshi Mitsubuchi
- Department of Pediatrics, Kumamoto University Graduate School of Medical Science, Kumamoto, Japan
| | - Hironao Numabe
- Department of Genetic Counseling, Faculty of Core Research, Ochanomizu University, Tokyo, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa, Japan
| | - Akira Hata
- Department of Public Health, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Issei Imoto
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
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Hayashi S, Yagi M, Morisaki I, Inazawa J. Identical deletion at 14q13.3 including PAX9 and NKX2-1 in siblings from mosaicism of unaffected parent. J Hum Genet 2015; 60:203-6. [DOI: 10.1038/jhg.2014.123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 01/19/2023]
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Quinonez SC, Park JM, Rabah R, Owens KM, Yashar BM, Glover TW, Keegan CE. 9p partial monosomy and disorders of sex development: Review and postulation of a pathogenetic mechanism. Am J Med Genet A 2013; 161A:1882-96. [DOI: 10.1002/ajmg.a.36018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/27/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Shane C. Quinonez
- Department of Pediatrics, Division of Genetics; University of Michigan; Ann Arbor; Michigan
| | - John M. Park
- Department of Urology; University of Michigan; Ann Arbor; Michigan
| | - Raja Rabah
- Department of Pathology; University of Michigan; Ann Arbor; Michigan
| | - Kailey M. Owens
- Department of Pediatrics, Division of Genetics; University of Michigan; Ann Arbor; Michigan
| | - Beverly M. Yashar
- Department of Human Genetics; University of Michigan; Ann Arbor; Michigan
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Chen CP, Su YN, Chern SR, Hsu CY, Tsai FJ, Wu PC, Lee CC, Chen YT, Lee MS, Wang W. Inv dup del(9p): prenatal diagnosis and molecular cytogenetic characterization by fluorescence in situ hybridization and array comparative genomic hybridization. Taiwan J Obstet Gynecol 2011; 50:67-73. [PMID: 21482378 DOI: 10.1016/j.tjog.2011.01.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2010] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE To present molecular cytogenetic characterization of prenatally detected inverted duplication and deletion of 9p, or inv dup del(9p). MATERIALS, METHODS, AND RESULTS A 35-year-old primigravid woman underwent amniocentesis at 16 weeks of gestation because of advanced maternal age. Amniocentesis revealed a derivative chromosome 9, or der(9) with additional material at the end of the short arm of one chromosome 9. Parental karyotypes were normal. Level II ultrasound showed ventriculomegaly and normal male external genitalia. Repeated amniocentesis was performed at 20 weeks of gestation. Array comparative genomic hybridization revealed a 0.70-Mb deletion at 9p24.3 and an 18.36-Mb duplication from 9p24.3 to 9p22.1. The distal 9p deletion encompassed the genes of DOCK8, ANKRD15, FOXD4, DMRT1, and DMRT3. Fluorescence in situ hybridization analysis using bacterial artificial chromosome clone probes specific for 9p confirmed that the der(9) was derived from the inv dup del(9p). The karyotype of the fetus was 46,XY,inv dup del(9)(:p22.1-->p24.3::p24.3-->qter)dn or 46,XY,der(9) del(9)(p24.3) inv dup(9)(p22.1p24.3)dn. Polymorphic DNA marker analysis determined a maternal origin of the inv dup del(9p). A 512-g male fetus was subsequently terminated at 22 weeks of gestation with facial dysmorphism. The fetus had normal male external genitalia without sex reversal. CONCLUSION Fluorescence in situ hybridization and array comparative genomic hybridization are useful to determine the nature of a prenatally detected aberrant chromosome derived from the inv dup del. Male fetuses with inv dup del(9p) and haploinsufficiency of DMRT1 and DMRT3 may present normal male external genitalia without sex reversal.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan.
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8
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Novel intragenic duplications and mutations of CASK in patients with mental retardation and microcephaly with pontine and cerebellar hypoplasia (MICPCH). Hum Genet 2011; 131:99-110. [DOI: 10.1007/s00439-011-1047-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 06/15/2011] [Indexed: 01/15/2023]
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9
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Complex Chromosome Rearrangement 46,XY, der(9)t(Y;9)(q12;p23) in a Girl With Sex Reversal and Mental Retardation. Urology 2011; 77:1213-6. [DOI: 10.1016/j.urology.2010.07.473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 07/06/2010] [Accepted: 07/20/2010] [Indexed: 12/11/2022]
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10
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Hayashi S, Imoto I, Aizu Y, Okamoto N, Mizuno S, Kurosawa K, Okamoto N, Honda S, Araki S, Mizutani S, Numabe H, Saitoh S, Kosho T, Fukushima Y, Mitsubuchi H, Endo F, Chinen Y, Kosaki R, Okuyama T, Ohki H, Yoshihashi H, Ono M, Takada F, Ono H, Yagi M, Matsumoto H, Makita Y, Hata A, Inazawa J. Clinical application of array-based comparative genomic hybridization by two-stage screening for 536 patients with mental retardation and multiple congenital anomalies. J Hum Genet 2010; 56:110-24. [DOI: 10.1038/jhg.2010.129] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Xu H, Miki K, Ishibashi S, Inoue J, Sun L, Endo S, Sekiya I, Muneta T, Inazawa J, Dezawa M, Mizusawa H. Transplantation of neuronal cells induced from human mesenchymal stem cells improves neurological functions after stroke without cell fusion. J Neurosci Res 2010; 88:3598-609. [DOI: 10.1002/jnr.22501] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 06/26/2010] [Accepted: 07/22/2010] [Indexed: 01/19/2023]
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12
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Piccione M, Antona V, Antona R, Gambino G, Pierluigi M, Malacarne M, Cavani S, Corsello G. Array-CGH defined chromosome 1p duplication in a patient with autism spectrum disorder, mild mental deficiency, and minor dysmorphic features. Am J Med Genet A 2010; 152A:486-9. [PMID: 20101695 DOI: 10.1002/ajmg.a.33212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maria Piccione
- Unità Operativa di Pediatria e Terapia Intensiva Neonatale, Dipartimento Materno Infantile, Università degli Studi di Palermo, Palermo, Italy
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Haldeman-Englert CR, Chapman KA, Kruger H, Geiger EA, McDonald-McGinn DM, Rappaport E, Zackai EH, Spinner NB, Shaikh TH. A de novo 8.8-Mb deletion of 21q21.1-q21.3 in an autistic male with a complex rearrangement involving chromosomes 6, 10, and 21. Am J Med Genet A 2010; 152A:196-202. [PMID: 20034085 PMCID: PMC2801886 DOI: 10.1002/ajmg.a.33176] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report here on a normal-appearing male with pervasive developmental disorder who was found to have a de novo, apparently balanced complex rearrangement involving chromosomes 6, 10, and 21: 46,XY,ins(21;10)(q11.2;p11.2p13)t(6;21)(p23;q11.2). Further analysis by high-density oligonucleotide microarray was performed, showing an 8.8-Mb heterozygous deletion at 21q21.1-q21.3. Interestingly, the deletion is distal to the translocation breakpoint on chromosome 21. The deletion involves 19 genes, including NCAM2 and GRIK1, both of which are associated with normal brain development and function, and have been considered as possible candidate genes in autism and other neurobehavioral disorders. This case underscores the utility of genomewide microarray analysis for the detection of copy number alterations in patients with apparently balanced complex rearrangements and abnormal phenotypes.
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Affiliation(s)
| | - Kimberly A. Chapman
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hillary Kruger
- Division of Child Development, Rehabilitation Medicine, and Metabolic Disease, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth A. Geiger
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Eric Rappaport
- Nucleic Acid and Protein Core, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elaine H. Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Nancy B. Spinner
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Tamim H. Shaikh
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA
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Hanemaaijer N, Dijkhuizen T, Haadsma M, Boeve M, Boon M, Hordijk R, Kok K, Sikkema-Raddatz B, van Ravenswaaij-Arts CMA. A 649 kb microduplication in 1p34.1, including POMGNT1, in a patient with microcephaly, coloboma and laryngomalacia; and a review of the literature. Eur J Med Genet 2009; 52:116-9. [PMID: 19452620 DOI: 10.1016/j.ejmg.2009.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We report on a male patient with intra-uterine growth retardation, microcephaly, coloboma, laryngomalacia and developmental delay. Array CGH analysis revealed a 649 kb duplication on chromosome 1p34.1. Only five patients with overlapping duplications have been reported thus far. Ten known genes are located in the duplicated region, including the POMGNT1 gene encoding for O-mannose beta-1,2-N-acetylglucosaminyltransferase. This gene, mutated in muscle-eye-brain disease, might be causative for the observed phenotype in our patient.
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Affiliation(s)
- Nicolien Hanemaaijer
- Department of Genetics, CB50, University Medical Centre Groningen, University of Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands
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Characterization of deletions at 9p affecting the candidate regions for sex reversal and deletion 9p syndrome by MLPA. Eur J Hum Genet 2009; 17:1439-47. [PMID: 19417767 DOI: 10.1038/ejhg.2009.70] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The distal region on the short arm of chromosome 9 is of special interest for scientists interested in sex development as well as in the clinical phenotype of patients with the 9p deletion syndrome, characterized by mental retardation, trigonocephaly and other dysmorphic features. Specific genes responsible for different aspects of the phenotype have not been identified. Distal 9p deletions have also been reported in patients with 46,XY sex reversal, with or without 9p deletion syndrome. Within this region the strongest candidates for the gonadal dysgenesis phenotype are the DMRT genes; however, the genetic mechanism is not clear yet. Multiple ligation-dependent probe amplification represents a useful technique to evaluate submicroscopic interstitial or distal deletions that would help the definition of the minimal sex reversal region on 9p and could lead to the identification of gene(s) responsible of the 46,XY gonadal disorders of sex development (DSD). We designed a synthetic probe set that targets genes within the 9p23-9p24.3 region and analyzed a group of XY patients with impaired gonadal development. We characterized a deletion distal to the DMRT genes in a patient with isolated 46,XY gonadal DSD and narrowed down the breakpoint in a patient with a 46,XY del(9)(p23) karyotype with gonadal DSD and mild symptoms of 9p deletion syndrome. The results are compared with other patients described in the literature, and new aspects of sex reversal and the 9p deletion syndrome candidate regions are discussed.
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16
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Hayashi S, Okamoto N, Makita Y, Hata A, Imoto I, Inazawa J. Heterozygous deletion at 14q22.1-q22.3 including the BMP4 gene in a patient with psychomotor retardation, congenital corneal opacity and feet polysyndactyly. Am J Med Genet A 2008; 146A:2905-10. [PMID: 18925664 DOI: 10.1002/ajmg.a.32519] [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
Here we report on a 1-year-old Japanese girl with psychomotor retardation, bilateral congenital corneal opacity and bilateral postaxial polysyndactyly of the feet. Although she had a normal female karyotype, our in-house bacterial artificial chromosome (BAC)-based array-CGH analysis successfully detected at least a 2.7-Mb heterozygous deletion at 14q22.1-q22.3 harboring 18 protein-coding genes. Among the genes, BMP4 was a candidate for the gene causing the abnormalities of both the eye and digits. It was previously reported that the BMP family was correlated with the morphogenesis of digits and ocular development, and Bmp4 heterozygous null mice revealed skeletal abnormalities including polydactyly and ocular anterior segment abnormalities. Patients with a deletion including BMP4 also hadabnormalities of the eye and digits. These previous reports support that a haplo-insufficiency of the BMP4 gene likely caused the congenital ocular and digit abnormalities. Moreover, among the other genes contained in the deletion, GMFB is a candidate for the gene responsible for the psychomotor retardation.
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Affiliation(s)
- Shin Hayashi
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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17
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Hayashi S, Mizuno S, Migita O, Okuyama T, Makita Y, Hata A, Imoto I, Inazawa J. TheCASKgene harbored in a deletion detected by array-CGH as a potential candidate for a gene causative of X-linked dominant mental retardation. Am J Med Genet A 2008; 146A:2145-51. [DOI: 10.1002/ajmg.a.32433] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Sismani C, Kitsiou-Tzeli S, Ioannides M, Christodoulou C, Anastasiadou V, Stylianidou G, Papadopoulou E, Kanavakis E, Kosmaidou-Aravidou Z, Patsalis PC. Cryptic genomic imbalances in patients with de novo or familial apparently balanced translocations and abnormal phenotype. Mol Cytogenet 2008; 1:15. [PMID: 18644119 PMCID: PMC2516517 DOI: 10.1186/1755-8166-1-15] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 07/21/2008] [Indexed: 11/23/2022] Open
Abstract
Background Carriers of apparently balanced translocations are usually phenotypically normal; however in about 6% of de novo cases, an abnormal phenotype is present. In the current study we investigated 12 patients, six de novo and six familial, with apparently balanced translocations and mental retardation and/or congenital malformations by applying 1 Mb resolution array-CGH. In all de novo cases, only the patient was a carrier of the translocation and had abnormal phenotype. In five out of the six familial cases, the phenotype of the patient was abnormal, although the karyotype appeared identical to other phenotypically normal carriers of the family. In the sixth familial case, all carriers of the translocations had an abnormal phenotype. Results Chromosomal and FISH analyses suggested that the rearrangements were "truly balanced" in all patients. However, array-CGH, revealed cryptic imbalances in three cases (3/12, 25%), two de novo (2/12, 33.3%) and one familial (1/12, 16.6%). The nature and type of abnormalities differed among the cases. In the first case, what was identified as a de novo t(9;15)(q31;q26.1), a complex rearrangement was revealed involving a ~6.1 Mb duplication on the long arm of chromosome 9, an ~10 Mb deletion and an inversion both on the long arm of chromosome 15. These imbalances were located near the translocation breakpoints. In the second case of a de novo t(4;9)(q25;q21.2), an ~6.6 Mb deletion was identified on the short arm of chromosome 7 which is unrelated to the translocation. In the third case, of a familial, t(4;7)(q13.3;p15.3), two deletions of ~4.3 Mb and ~2.3 Mb were found, each at one of the two translocation breakpoints. In the remaining cases the translocations appeared balanced at 1 Mb resolution. Conclusion This study investigated both de novo and familial apparently balanced translocations unlike other relatively large studies which are mainly focused on de novo cases. This study provides additional evidence that cryptic genomic imbalances are common in patients with abnormal phenotype and "apparently balanced" translocations not only in de novo but can also occur in familial cases. The use of microarrays with higher resolution such as oligo-arrays may reveal that the frequency of cryptic genomic imbalances among these patients is higher.
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Affiliation(s)
- Carolina Sismani
- Department of Cytogenetics, The Cyprus Institute of Neurology and Genetics Nicosia, Cyprus.
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Tokutomi T, Hayashi S, Imai K, Chida A, Ishiwata T, Asano Y, Inazawa J, Nonoyama S. dup(8p)/del(8q) recombinant chromosome in a girl with hepatic focal nodular hyperplasia. Am J Med Genet A 2008; 143A:1334-7. [PMID: 17506094 DOI: 10.1002/ajmg.a.31770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A 15-year-old girl had exertion dyspnea, focal nodular hyperplasia of the liver, portal vein hypoplasia, portopulmonary hypertension, mental retardation, and minor facial abnormalities. Cytogenetic analysis demonstrated an abnormal chromosome 8 with 8p22-pter duplication and 8q24.3-qter deletion, with the duplicated 8p segment attached to band 8q24.3. Her mother had a pericentric inversion of chromosome 8, inv(8)(p22q24.3). Therefore, the girl's abnormal chromosome 8 was a recombinant of maternal inversion chromosome: 46,XX,rec(8)dup(8p)inv(8)(p22q24.3)mat. Further characterization of the recombinant chromosome, using array CGH and regional FISH analyses, defined 15 Mb distal 8p duplication and 0.5 Mb 8q deletion. Possible correlation of the recombinant chromosome and hepatic focal nodular hyperplasia in the patient is discussed.
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Affiliation(s)
- Tomoharu Tokutomi
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Saitama, Japan.
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20
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Identification of origin of unknown derivative chromosomes by array-based comparative genomic hybridization using pre- and postnatal clinical samples. J Hum Genet 2007; 52:934-942. [PMID: 17940726 DOI: 10.1007/s10038-007-0199-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 09/08/2007] [Indexed: 02/04/2023]
Abstract
Microarray-based comparative genomic hybridization (array CGH) is a high-resolution and comprehensive method for detecting both genome-wide and chromosome-specific copy-number imbalance. We have developed an array CGH analysis system (consisting of an array CGH chip plus its exclusive analysis software) for constitutional genetic diagnosis and have evaluated the suitability of our system for molecular diagnosis using pre- and postnatal clinical samples. In a blind study, each of the 264 sample karyotypes identified by array CGH analysis was consistent with that identified by traditional karyotype analysis--with one exception, case (47, XXX)--and we were able to identify origins, such as small supernumerary marker chromosomes, which cannot be determined by conventional cytogenetics. We also acquired very accurate, fast and reliable results using a diminutive amount of clinical samples. Taken together, the array CGH platform developed in this study is a rapid, powerful and sensitive technology for pre- and postnatal diagnosis using a very small amount of clinical sample.
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Aradhya S, Cherry AM. Array-based comparative genomic hybridization: clinical contexts for targeted and whole-genome designs. Genet Med 2007; 9:553-9. [PMID: 17873642 DOI: 10.1097/gim.0b013e318149e354] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Array-based comparative genomic hybridization is ushering in a new standard for analyzing the genome, overcoming the limits of resolution associated with conventional G-banded karyotyping. The first genomic arrays were based on bacterial artificial chromosome clones mapped during the initial phases of the Human Genome Project. These arrays essentially represented multiple fluorescence in situ hybridization assays performed simultaneously. The first arrays featured a targeted design, consisting of hundreds of bacterial artificial chromosome clones limited mostly to genomic regions of known medical significance. Then came whole-genome arrays, which contained bacterial artificial chromosome clones from across the entire genome. More recently, alternative designs based on oligonucleotide probes have been developed, and all these are high-density whole-genome arrays with resolutions between 3 and 35 kb. Certain clinical circumstances are well suited for investigation by targeted arrays, and there are others in which high-resolution whole-genome arrays are necessary. Here we review the differences between the two types of arrays and the clinical contexts for which they are best suited. As array-based comparative genomic hybridization is integrated into diagnostic laboratories and different array designs are used in appropriate clinical contexts, this novel technology will invariably alter the testing paradigm in medical genetics and will lead to the discovery of novel genetic conditions caused by chromosomal anomalies.
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Affiliation(s)
- Swaroop Aradhya
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA.
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22
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Hayashi S, Ono M, Makita Y, Imoto I, Mizutani S, Inazawa J. Fortuitous detection of a submicroscopic deletion at 1q25 in a girl with Cornelia-de Lange syndrome carrying t(5;13)(p13.1;q12.1) by array-based comparative genomic hybridization. Am J Med Genet A 2007; 143A:1191-7. [PMID: 17497725 DOI: 10.1002/ajmg.a.31737] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report on a 2-year-old Japanese girl with Cornelia-de Lange syndrome (CdLS) who had mental and growth retardation, together with characteristic facial anomalies and mild extremity malformations. She had a balanced chromosomal translocation, 46,XX,t(5;13)(p13.1;q12.1) de novo. Surprisingly, this was the same translocation that had provided a clue to the identification of a major causative gene for CdLS, NIPBL [Krantz et al., 2004; Tonkin et al., 2004]. Using fluorescence in situ hybridization (FISH), the breakpoint was confirmed to lie within NIPBL at 5p13.1. Furthermore, array-based comparative genomic hybridization (array-CGH) demonstrated a cryptic 1-Mb deletion harboring six known genes at 1q25-q31.1. A FISH analysis of her parents confirmed that the deletion was de novo. Although patients with interstitial deletions at 1q are rare, some of their features were similar to those observed in our patient, indicating that her clinical manifestations are likely to be affected by not only the disruption of NIPBL but also the concomitant microdeletion at 1q25-q31.1. The present case suggests that array-CGH can uncover cryptic genomic aberrations affecting atypical phenotypes even in well-known congenital disorders.
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MESH Headings
- Child, Preschool
- Chromosome Banding
- Chromosome Breakage
- Chromosome Deletion
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 5/genetics
- De Lange Syndrome/genetics
- Female
- Genome, Human/genetics
- Humans
- In Situ Hybridization, Fluorescence/methods
- Oligonucleotide Array Sequence Analysis
- Translocation, Genetic
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Affiliation(s)
- Shin Hayashi
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, and Department of Pediatrics, Tokyo Teishin Hospital, Tokyo, Japan
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23
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Callier P, Faivre L, Marle N, Thauvin-Robinet C, Mosca AL, Masurel-Paulet A, Borgnon J, Falcon-Eicher S, Danino A, Malka G, Le Merrer M, Huet F, Mugneret F. Untreated growth hormone deficiency with extremely short stature, bone dysplasia, cleft lip--palate and severe mental retardation in a 26-year-old man with a de novo unbalanced translocation t(1;12)(q24;q24). Eur J Med Genet 2007; 50:455-64. [PMID: 17720646 DOI: 10.1016/j.ejmg.2007.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 06/26/2007] [Indexed: 10/23/2022]
Abstract
We report on a 26-year-old patient presenting with extremely short stature (height 72cm, weight 6.5kg, OFC 42.5cm), facial dysmorphism, cleft lip--palate, severe mental retardation and de novo 1q24.2--q25.2 and 12q24.31 interstitial deletion. He was the only child of non-consanguineous parents and his birth length was 43cm. He had severe feeding difficulties and required enteral nutrition until the age of 3 years. Standard cytogenetic analysis showed an apparently balanced de novo translocation t(1;12)(q24;q24). Endocrine studies at 11 years of age for severe growth retardation revealed multiple pituitary hormone deficiency with severe growth hormone deficiency, but the child was untreated because of associated mental retardation. At 26 years of age, he could not walk or speak and had no signs of puberty. Investigations revealed spondylo-epi-metaphyseal dysplasia with severe osteoporosis, enlarged aorta when compared to the patient's size and apparently normal pituitary development. High resolution karyotype showed a 1q24-q25 deletion, and comparative genomic hybridization studies confirmed the 1q interstitial deletion. FISH studies of both breakpoints using PACs and BACs enabled us to further characterize the 1q interstitial deletion (1q24.2-1q25.2) and also revealed a 12q24.31 interstitial microdeletion. This case is compared with previously reported patients with similar deletions, but the untreated pituitary deficiency could also be responsible in part for the severity of the growth deficiency. This observation is of interest for two reasons. First, these deletions could be a clue in the search for a gene responsible for growth hormone deficiency/midline defects. Second, it shows the importance of molecular cytogenetics in the study of de novo apparently balanced translocation with abnormal phenotype.
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Affiliation(s)
- P Callier
- Laboratoire de Cytogénétique, Département de Génétique, CHU Le Bocage, 2 Bd Maréchal de Lattre de Tassigny, 21034 Dijon cédex, France.
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24
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Hayashi S, Honda S, Minaguchi M, Makita Y, Okamoto N, Kosaki R, Okuyama T, Imoto I, Mizutani S, Inazawa J. Construction of a high-density and high-resolution human chromosome X array for comparative genomic hybridization analysis. J Hum Genet 2007; 52:397-405. [PMID: 17406783 DOI: 10.1007/s10038-007-0127-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Accepted: 02/01/2007] [Indexed: 10/23/2022]
Abstract
The human chromosome X is closely associated with congenital disorders and mental retardation (MR), because it contains a significantly higher number of genes than estimated from the proportion in the human genome. We constructed a high-density and high-resolution human chromosome X array (X-tiling array) for comparative genomic hybridization (CGH). The array contains a total of 1,001 bacterial artificial chromosome (BACs) throughout chromosome X except pseudoautosomal regions and two BACs specific for Y. In four hybridizations using DNA samples from healthy males, the ratio of each spotted DNA was scattered between -3SD and 3SD, corresponding to a log(2) ratio of -0.35 and 0.35, respectively. Using DNA samples from patients with known congenital disorders, our X-tiling array was proven to discriminate one-copy losses and gains together with their physical sizes, and also to estimate the percentage of a mosaicism in a patient with mos 45,X[13]/46,X,r(X)[7]. Furthermore, array-CGH in a patient with atypical Schinzel-Giedion syndrome disclosed a 1.1-Mb duplication at Xq22.3 including a part of the IL1RAPL2 gene as a likely causative aberration. The results indicate our in-house X-tiling array to be useful for the identification of cryptic copy-number aberrations containing novel genes responsible for diseases such as congenital disorders and X-linked MR.
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Affiliation(s)
- Shin Hayashi
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Department of Pediatric and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo, 113-8510, Japan
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Corporation (JST), 4-1-8 Hon-machi Kawaguchi, Saitama, 332-0012, Japan
| | - Shozo Honda
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Department of Pediatric and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo, 113-8510, Japan
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Corporation (JST), 4-1-8 Hon-machi Kawaguchi, Saitama, 332-0012, Japan
| | - Maki Minaguchi
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Corporation (JST), 4-1-8 Hon-machi Kawaguchi, Saitama, 332-0012, Japan
| | - Yoshio Makita
- Department of Pediatrics, Asahikawa Medical Collage, Midorigaoka-Higashi 2-1-1-1, Asahikawa, 078-8510, Japan
| | - Nobuhiko Okamoto
- Department of Planning and Research, Osaka Medical Center and Research Institute for Maternal and Child Health, Murodocho 840, Izumi, Osaka, Japan
| | - Rika Kosaki
- Department of Clinical Genetics and Molecular Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Torayuki Okuyama
- Department of Clinical Genetics and Molecular Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Issei Imoto
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Hard Tissue Genome Research Center, Tokyo Medical and Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo, 113-8510, Japan
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Corporation (JST), 4-1-8 Hon-machi Kawaguchi, Saitama, 332-0012, Japan
| | - Shuki Mizutani
- Department of Pediatric and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Hard Tissue Genome Research Center, Tokyo Medical and Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo, 113-8510, Japan.
- 21st Century Center of Excellence Program for Molecular Destruction and Reconstitution of Tooth and Bone, Tokyo Medical and Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo, 113-8510, Japan.
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Corporation (JST), 4-1-8 Hon-machi Kawaguchi, Saitama, 332-0012, Japan.
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Jeon JP, Shim SM, Nam HY, Baik SY, Kim JW, Han BG. Copy number increase of 1p36.33 and mitochondrial genome amplification in Epstein-Barr virus-transformed lymphoblastoid cell lines. ACTA ACUST UNITED AC 2007; 173:122-30. [PMID: 17321327 DOI: 10.1016/j.cancergencyto.2006.10.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 10/17/2006] [Accepted: 10/19/2006] [Indexed: 11/22/2022]
Abstract
Array CGH has been applied to detect chromosomal aberrations in cancer and genetic diseases. Epstein-Barr virus (EBV)-infected B lymphocytes are transformed to continuously proliferating lymphoblastoid cell lines (LCLs), which are a very common genome resource for human genetic studies. We used bacterial artificial chromosome (BAC) array CGH to assess a chromosomal aberration of LCLs in EBV-induced B-cell transformation. At early passages, LCLs exhibited a greater copy number variation in 1p36.33 compared to primary B-cells. Quantitative polymerase chain reaction (PCR) confirmed the increase in the copy number in 1p36.33. Because a segment of 1p36.33 is nearly identical to a part of the mitochondrial DNA, this increase was attributed to an increase in the copy number of mitochondrial DNA. The expression levels of mitochondrial biogenesis-related genes were elevated in the LCLs, which is consistent with the increased copy numbers of mitochondrial DNA, suggesting that increased mitochondrial biogenesis is indicative of the progression of EBV-mediated B-cell transformation. In addition, our array CGH of LCLs revealed potential copy number polymorphisms of chromosomal segments among Korean populations. Taken together, these findings suggest that LCLs in the early passages preserve the chromosomal integrity of primary B-cells at the cytogenetic level during EBV-transformed B-cell immortalization, except for a copy number variation in 1p36.33 due to increased mitochondrial DNA copy numbers. Thus, analyses of array CGH profiles of diseases should take into account the potential for copy number variation of 1p36.33.
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MESH Headings
- Aneuploidy
- Cell Line, Transformed
- Cell Transformation, Viral/genetics
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Human, Pair 1/genetics
- DNA, Mitochondrial/genetics
- Gene Amplification
- Gene Expression
- Genome, Human/genetics
- Herpesvirus 4, Human/physiology
- Humans
- Lymphocytes/metabolism
- Lymphocytes/pathology
- Lymphocytes/virology
- Microarray Analysis/methods
- Mitochondrial Proteins/genetics
- Nucleic Acid Hybridization/methods
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
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Affiliation(s)
- Jae-Pil Jeon
- BioBank for Health Sciences, Center for Genome Science, National Institute of Health, Korea Center for Disease Control and Prevention, 5 Nokbun, Eunpyung-Gu, Seoul 122-701, Republic of Korea
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26
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Honda S, Hayashi S, Kato M, Niida Y, Hayasaka K, Okuyama T, Imoto I, Mizutani S, Inazawa J. Clinical and molecular cytogenetic characterization of two patients with non-mutational aberrations of theFMR2 gene. Am J Med Genet A 2007; 143A:687-93. [PMID: 17343270 DOI: 10.1002/ajmg.a.31638] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report on two patients; a female having mild mental retardation (MR) with a balanced translocation, 46,XX,t(X;15)(q28;p11.2), and a male diagnosed as having mucopolysaccharidosis type II (MPS II or Hunter syndrome) with atypical early-onset MR and a normal male karyotype. Molecular cytogenetic analyses, including fluorescence in situ hybridization and array-based comparative genomic hybridization using an in-house X-tiling array, revealed that first patient to have a breakpoint at Xq28 lying within the FMR2 gene and the second to have a small deletion at Xq28 including part of FMR2 together with the IDS gene responsible for MPS II. In Patient 1, X-chromosome inactivation predominantly occurred in the normal X in her lymphocytes, suggesting that her MR might be explained by a disruption of the FMR2 gene on der(X) t(X;15) concomitant with the predominant inactivation of the intact FMR2 gene in another allele. We compared phenotypes of Patient 2 with those of MPS II cases with deletion of the IDS gene alone reported previously, suggesting that the early-onset MR might be affected by the additional deletion of FMR2.
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Affiliation(s)
- Shozo Honda
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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27
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Okamoto N, Kubota T, Nakamura Y, Murakami R, Nishikubo T, Tanaka I, Takahashi Y, Hayashi S, Imoto I, Inazawa J, Hosokai N, Kohsaka S, Uchino S. 22q13 microduplication in two patients with common clinical manifestations: A recognizable syndrome? Am J Med Genet A 2007; 143A:2804-9. [DOI: 10.1002/ajmg.a.31771] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Chiyonobu T, Hayashi S, Kobayashi K, Morimoto M, Miyanomae Y, Nishimura A, Nishimoto A, Ito C, Imoto I, Sugimoto T, Jia Z, Inazawa J, Toda T. Partial tandem duplication ofGRIA3 in a male with mental retardation. Am J Med Genet A 2007; 143A:1448-55. [PMID: 17568425 DOI: 10.1002/ajmg.a.31798] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genetic factors underlying mental retardation (MR) are very heterogeneous. Recent studies have identified a number of genes involved in MR, several of which lie on the X-chromosome, but the current understanding of the monogenic causes of MR is far from complete. Investigation of chromosomal rearrangements in patients with MR has proven particularly informative in the search for novel genes. Using array-based comparative genomic hybridization analysis, we identified a small copy number gain at Xq25, which was undetectable by conventional G-band analysis, in a boy with unexplained MR. Further characterization revealed a partial tandem duplication of GRIA3, an alteration also present on one allele in his mother. RT-PCR analysis of lymphoblastoid cell RNA revealed remarkably reduced GRIA3 transcript levels in the patient. The mother, whose cognitive level is normal, also demonstrated remarkably reduced GRIA3 transcript levels in lymphoblastoid cells, and X-chromosome inactivation (XCI) was completely skewed in her peripheral lymphocytes. It is possible that XCI in the brain is not completely skewed and that GRIA3 expression from the normal allele may account for the mother's normal cognitive function. Taken together with previous findings of GRIA3 disruptions in the patients with MR, our study strengthens the idea that GRIA3 is a candidate gene for X-linked MR and that severely reduced GRIA3 expression results in MR.
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Affiliation(s)
- Tomohiro Chiyonobu
- Division of Clinical Genetics, Department of Medical Genetics, Osaka University Graduate School of Medicine, 2-2-B9 Yamadaoka, Suita, Osaka 565-0871, Japan
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29
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Lennon PA, Boerkoel CF, Plunkett K, Soukam S, Cheung SW, Patel A. A novel 8.5 MB dup(1)(p34.1p34.3) characterized by FISH in a child presenting with congenital heart defect and dysmorphic features. Am J Med Genet A 2006; 140A:1864-70. [PMID: 16892326 DOI: 10.1002/ajmg.a.31392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Chromosome duplications involving 1p are rarely reported but are apparently associated with short survival as well as congenital malformations and impaired development. Several of these have had congenital heart defects, although too few patients have been reported with similar breakpoints to characterize a syndrome. We present a girl with a novel interstitial duplication in the short arm of chromosome 1 [46,XX,dup(1)(p34.1p34.3)]. She presented with congenital heart defects at 1 month and by 1 year of age manifested delayed acquisition of motor milestones and subsequently of language milestones. By breakpoint-mapping using FISH analysis, we determined that her 1p duplication spans 8.5 megabases. Her 1p duplication is the smallest reported to date to contain 1p34 in patients with congenital heart defect due to abnormalities of heart looping during development. Thus, her 8.5 MB duplication provides a target region to search for a potentially dosage-sensitive gene(s) causing abnormal heart looping when duplicated. Two patients have been reported with duplication including 1p34 but without congenital heart defect, and their duplications span all but the distal approximately 2 MB segment duplicated in our patient. Thus, within our patient's 8.5 MB target region for a dosage sensitive gene leading to looping abnormalities (and thereby congenital heart defect), the distal 2 MB region might well be the region to begin the search.
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Affiliation(s)
- P A Lennon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77021, USA
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