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Miclea D, Osan S, Bucerzan S, Stefan D, Popp R, Mager M, Puiu M, Zimbru C, Chirita-Emandi A, Alkhzouz C. Copy number variation analysis in 189 Romanian patients with global developmental delay/intellectual disability. Ital J Pediatr 2022; 48:207. [PMID: 36585697 PMCID: PMC9801529 DOI: 10.1186/s13052-022-01397-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 12/13/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Developmental delay and intellectual disability represent a common pathology in general population, involving about 3% of the pediatric age population, the genetic etiology being often involved. The aim of this study was to determine the clinically relevant copy number variants in patients diagnosed with global developmental delay/intellectual disability in our population, using the chromosomal microarray analysis. METHODS We analyzed 189 patients diagnosed with global developmental delay/intellectual disability, presented in Clinical Emergency Hospital for Children, Cluj-Napoca. The patients were completely clinically investigated, including dysmorphic and internal malformations evaluation, psychiatric, neuropsychological and metabolic evaluation, standard karyotyping. Genomic analysis was done using chromosomal microarray analysis. RESULTS Pathogenic findings (including uniparental disomy) and variants of unknown significance were detected in 53 of 189 patients (28.04%). Pathogenic copy number variants and uniparental disomy were observed in 35 of 189 patients (18.51%). Two patients presented uniparental disomy for chromosome 15, one with clinical phenotype of Prader-Willi syndrome and the other with clinical phenotype with Angelman syndrome. Within the category of pathogenic findings, the recurrent copy number variants were seen in 21 of 35 patients (60%). CONCLUSIONS The increased percentage of pathogenic structural variants observed in patients with global developmental delay/intellectual disability analyzed by chromosomal microarray technique supports its use in patients with a non-specific phenotype such as these neurodevelopmental disorders. The high percentage of recurrent pathogenic variants between these findings is a finding that support their initial evaluation when a genetic testing algorithm could be a useful option.
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Affiliation(s)
- Diana Miclea
- grid.411040.00000 0004 0571 5814Department of Molecular Sciences, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur Street, No 6, 400349 Cluj-Napoca, Romania ,Emergency Clinical Hospital for Children, Pasteur Street, No 6, 400349 Cluj-Napoca, Romania
| | - Sergiu Osan
- grid.411040.00000 0004 0571 5814Department of Molecular Sciences, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur Street, No 6, 400349 Cluj-Napoca, Romania
| | - Simona Bucerzan
- Emergency Clinical Hospital for Children, Pasteur Street, No 6, 400349 Cluj-Napoca, Romania ,grid.411040.00000 0004 0571 5814Department of Mother and Child, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Delia Stefan
- grid.411040.00000 0004 0571 5814Department of Molecular Sciences, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur Street, No 6, 400349 Cluj-Napoca, Romania
| | - Radu Popp
- grid.411040.00000 0004 0571 5814Department of Molecular Sciences, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur Street, No 6, 400349 Cluj-Napoca, Romania
| | - Monica Mager
- Emergency Clinical Hospital for Children, Pasteur Street, No 6, 400349 Cluj-Napoca, Romania ,grid.411040.00000 0004 0571 5814Department of Neuroscience, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Maria Puiu
- grid.22248.3e0000 0001 0504 4027“Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Cristian Zimbru
- grid.6992.40000 0001 1148 0861Polytechnic University, Timisoara, Romania
| | - Adela Chirita-Emandi
- grid.22248.3e0000 0001 0504 4027“Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Camelia Alkhzouz
- Emergency Clinical Hospital for Children, Pasteur Street, No 6, 400349 Cluj-Napoca, Romania ,grid.411040.00000 0004 0571 5814Department of Mother and Child, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Ben-Mahmoud A, Jun KR, Gupta V, Shastri P, de la Fuente A, Park Y, Shin KC, Kim CA, da Cruz AD, Pinto IP, Minasi LB, Silva da Cruz A, Faivre L, Callier P, Racine C, Layman LC, Kong IK, Kim CH, Kim WY, Kim HG. A rigorous in silico genomic interrogation at 1p13.3 reveals 16 autosomal dominant candidate genes in syndromic neurodevelopmental disorders. Front Mol Neurosci 2022; 15:979061. [PMID: 36277487 PMCID: PMC9582330 DOI: 10.3389/fnmol.2022.979061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.
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Affiliation(s)
- Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Ran Jun
- Department of Laboratory Medicine, Inje University Haeundae Paik Hospital, Busan, South Korea
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Pinang Shastri
- Department of Cardiovascular Medicine, Cape Fear Valley Medical Center, Fayetteville, NC, United States
| | - Alberto de la Fuente
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Yongsoo Park
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Chul Shin
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Chong Ae Kim
- Faculdade de Medicina, Unidade de Genética do Instituto da Criança – Hospital das Clínicas HCFMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Aparecido Divino da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Irene Plaza Pinto
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Lysa Bernardes Minasi
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Alex Silva da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental Disorders, Université de Bourgogne-Franche Comté, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d’Enfants, Dijon, France
| | - Patrick Callier
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Caroline Racine
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, United States
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- *Correspondence: Hyung-Goo Kim,
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Uehara DT, Mitsubuchi H, Inazawa J. A missense variant in NUF2, a component of the kinetochore NDC80 complex, causes impaired chromosome segregation and aneuploidy associated with microcephaly and short stature. Hum Genet 2021; 140:1047-1060. [PMID: 33721060 DOI: 10.1007/s00439-021-02273-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/28/2021] [Indexed: 12/11/2022]
Abstract
Mutations in proteins involved in cell division and chromosome segregation, such as microtubule-regulating, centrosomal and kinetochore proteins, are associated with microcephaly and/or short stature. In particular, the kinetochore plays an essential role in mitosis and cell division by mediating connections between chromosomal DNA and spindle microtubules. To date, only a few genes encoding proteins of the kinetochore complex have been identified as causes of syndromes that include microcephaly. We report a male patient with a rare de novo missense variant in NUF2, after trio whole-exome sequencing analysis. The patient presented with microcephaly and short stature, with additional features, such as bilateral vocal cord paralysis, micrognathia and atrial septal defect. NUF2 encodes a subunit of the NDC80 complex in the outer kinetochore, important for correct microtubule binding and spindle assembly checkpoint. The mutated residue is buried at the calponin homology (CH) domain at the N-terminus of NUF2, which interacts with the N-terminus of NDC80. The variant caused the loss of hydrophobic interactions in the core of the CH domain of NUF2, thereby impairing the stability of NDC80-NUF2. Analysis using a patient-derived lymphoblastoid cell line revealed markedly reduced protein levels of both NUF2 and NDC80, aneuploidy, increased micronuclei formation and spindle abnormality. Our findings suggest that NUF2 may be the first member of the NDC80 complex to be associated with a human disorder.
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Affiliation(s)
- Daniela Tiaki Uehara
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hiroshi Mitsubuchi
- Department of Neonatology, Kumamoto University Hospital, Kumamoto, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan.
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Ganna A, Verweij KJH, Nivard MG, Maier R, Wedow R, Busch AS, Abdellaoui A, Guo S, Sathirapongsasuti JF, Lichtenstein P, Lundström S, Långström N, Auton A, Harris KM, Beecham GW, Martin ER, Sanders AR, Perry JRB, Neale BM, Zietsch BP. Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior. Science 2019; 365:eaat7693. [PMID: 31467194 PMCID: PMC7082777 DOI: 10.1126/science.aat7693] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 07/22/2019] [Indexed: 12/11/2022]
Abstract
Twin and family studies have shown that same-sex sexual behavior is partly genetically influenced, but previous searches for specific genes involved have been underpowered. We performed a genome-wide association study (GWAS) on 477,522 individuals, revealing five loci significantly associated with same-sex sexual behavior. In aggregate, all tested genetic variants accounted for 8 to 25% of variation in same-sex sexual behavior, only partially overlapped between males and females, and do not allow meaningful prediction of an individual's sexual behavior. Comparing these GWAS results with those for the proportion of same-sex to total number of sexual partners among nonheterosexuals suggests that there is no single continuum from opposite-sex to same-sex sexual behavior. Overall, our findings provide insights into the genetics underlying same-sex sexual behavior and underscore the complexity of sexuality.
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Affiliation(s)
- Andrea Ganna
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Karin J H Verweij
- Department of Psychiatry, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 5, 1105 AZ Amsterdam, Netherlands
| | - Michel G Nivard
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT, Amsterdam, Netherlands
| | - Robert Maier
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robbee Wedow
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Sociology, Harvard University, Cambridge, MA 02138, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Sociology, University of Colorado, Boulder, CO 80309-0483, USA
- Health and Society Program and Population Program, Institute of Behavioral Science, University of Colorado, Boulder, CO 80309-0483, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309-0483, USA
| | - Alexander S Busch
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, Copenhagen, Denmark
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 5, 1105 AZ Amsterdam, Netherlands
| | - Shengru Guo
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | | | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Lundström
- Centre for Ethics, Law and Mental Health, Gillberg Neuropsychiatry Centre, University of Gothenburg, Sweden
| | - Niklas Långström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Kathleen Mullan Harris
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gary W Beecham
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Eden R Martin
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - Alan R Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem Research Institute, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - John R B Perry
- Medical Research Council (MRC) Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan P Zietsch
- Centre for Psychology and Evolution, School of Psychology, University of Queensland, St. Lucia, Brisbane QLD 4072, Australia.
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Villela D, Costa SS, Vianna-Morgante AM, Krepischi AC, Rosenberg C. Efficient detection of chromosome imbalances and single nucleotide variants using targeted sequencing in the clinical setting. Eur J Med Genet 2017; 60:667-674. [DOI: 10.1016/j.ejmg.2017.08.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 11/29/2022]
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Ozawa N, Sago H, Matsuoka K, Maruyama T, Migita O, Aizu Y, Inazawa J. Cytogenetic analysis of spontaneously discharged products of conception by array-based comparative genomic hybridization. SPRINGERPLUS 2016; 5:874. [PMID: 27386323 PMCID: PMC4920787 DOI: 10.1186/s40064-016-2594-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/15/2016] [Indexed: 12/12/2022]
Abstract
Background Cytogenetic analysis of products of conception (POC) is essential for the management of recurrent pregnancy loss (RPL), but the currently-performed G-banding method is not necessarily applicable to spontaneously discharged POC because of poor quality for culture. We analyzed the karyotypes of 15 spontaneously discharged POC by array-based comparative genomic hybridization (array-CGH). Results All specimens were successfully analyzed and 10 cases had abnormal results: gain in copy number (n = 7) and loss in copy number (n = 3). Most of them were estimated to be whole chromosome aneuploidy, whereas one case was compatible with microdeletion. Two cases were suspected to be male diploid contaminated by maternal DNA or triploid because of the unsatisfactory signal patterns on X/Y chromosomes. Two of three cases with normal female DNA pattern were identified to be contaminated with maternal DNA by the additional analysis of short tandem repeats. Conclusions Given the potential to analyze non-viable POC specimens, array-CGH is a feasible cytogenetic tool for women, in particular, with a history of RPL who desire non-surgical or expectant management of miscarriages and/or a thorough investigation on the cause for recurrent miscarriage, although it needs to take into account high incidence of maternal contamination in spontaneously discharged POC. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2594-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nobuaki Ozawa
- Center of Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535 Japan
| | - Haruhiko Sago
- Center of Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535 Japan
| | - Kentaro Matsuoka
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan ; Department of Pathology, Kitasato Institute Hospital, Tokyo, Japan
| | - Tetsuo Maruyama
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Ohsuke Migita
- Department of Clinical Genetics and Molecular Medicine, National Center for Child Health and Development, Tokyo, Japan ; Department of Clinical Genetics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshinori Aizu
- Division of Advanced Technology and Development, BML, Inc., Kawagoe, 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, Tokyo, Japan
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