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Wang Y, Wen X, Shen XM, Di L, Sun Y, Li Y, Zhang S, Wen Q, Wang J, Duo J, Huang Y, Lu Y, Xu M, Wang M, Chen H, Zhu W, Da Y. A rare complex structural variant of novel intragenic inversion combined with reciprocal translocation t(X;1)(p21.2;p13.3) in Duchenne muscular dystrophy. Neuromuscul Disord 2024; 39:24-29. [PMID: 38714145 DOI: 10.1016/j.nmd.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 05/09/2024]
Abstract
Structural variants (SVs) are infrequently observed in Duchenne muscular dystrophy (DMD), a condition mainly marked by deletions and point mutations in the DMD gene. SVs in DMD remain difficult to reliably detect due to the limited SV-detection capacity of conventionally used short-read sequencing technology. Herein, we present a family, a boy and his mother, with clinical signs of muscular dystrophy, elevated creatinine kinase levels, and intellectual disability. A muscle biopsy from the boy showed dystrophin deficiency. Routine molecular techniques failed to detect abnormalities in the DMD gene, however, dystrophin mRNA transcripts analysis revealed an absence of exons 59 to 79. Subsequent long-read whole-genome sequencing identified a rare complex structural variant, a 77 kb novel intragenic inversion, and a balanced translocation t(X;1)(p21.2;p13.3) rearrangement within the DMD gene, expanding the genetic spectrum of dystrophinopathy. Our findings suggested that SVs should be considered in cases where conventional molecular techniques fail to identify pathogenic variants.
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Affiliation(s)
- Yaye Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Xinmei Wen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Xin-Ming Shen
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
| | - Li Di
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yanan Sun
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yun Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Shu Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Qi Wen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Jingsi Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Jianying Duo
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yue Huang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yan Lu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Min Xu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Min Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Hai Chen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Wenjia Zhu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yuwei Da
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China.
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2
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Janzing AM, Eklund E, De Koning TJ, Eggink H. Clinical Characteristics Suggestive of a Genetic Cause in Cerebral Palsy: A Systematic Review. Pediatr Neurol 2024; 153:144-151. [PMID: 38382247 DOI: 10.1016/j.pediatrneurol.2024.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 01/11/2024] [Accepted: 01/27/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Cerebral palsy (CP) is a clinical diagnosis and was long categorized as an acquired disorder, but more and more genetic etiologies are being identified. This review aims to identify the clinical characteristics that are associated with genetic CP to aid clinicians in selecting candidates for genetic testing. METHODS The PubMed database was systematically searched to identify genes associated with CP. The clinical characteristics accompanying these genetic forms of CP were compared with published data of large CP populations resulting in the identification of potential indicators of genetic CP. RESULLTS Of 1930 articles retrieved, 134 were included. In these, 55 CP genes (described in two or more cases, n = 272) and 79 candidate genes (described in only one case) were reported. The most frequently CP-associated genes were PLP1 (21 cases), ARG1 (17 cases), and CTNNB1 (13 cases). Dyskinesia and the absence of spasticity were identified as strong potential indicators of genetic CP. Presence of intellectual disability, no preterm birth, and no unilateral distribution of symptoms were classified as moderate genetic indicators. CONCLUSIONS Genetic causes of CP are increasingly identified. The clinical characteristics associated with genetic CP can aid clinicians regarding to which individual with CP to offer genetic testing. The identified potential genetic indicators need to be validated in large CP cohorts but can provide the first step toward a diagnostic algorithm for genetic CP.
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Affiliation(s)
- Anna M Janzing
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Expertise Center Movement Disorders Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erik Eklund
- Faculty of Medicine, Department of Clinical Sciences, Pediatrics, Lund University, Lund, Sweden
| | - Tom J De Koning
- Expertise Center Movement Disorders Groningen, University Medical Center Groningen, Groningen, The Netherlands; Faculty of Medicine, Department of Clinical Sciences, Pediatrics, Lund University, Lund, Sweden; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hendriekje Eggink
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Expertise Center Movement Disorders Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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Pluta N, von Moers A, Pechmann A, Stenzel W, Goebel HH, Atlan D, Wolf B, Nanda I, Zaum AK, Rost S. Whole-Genome Sequencing Identified New Structural Variations in the DMD Gene That Cause Duchenne Muscular Dystrophy in Two Girls. Int J Mol Sci 2023; 24:13567. [PMID: 37686372 PMCID: PMC10488134 DOI: 10.3390/ijms241713567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Dystrophinopathies are the most common muscle diseases, especially in men. In women, on the other hand, a manifestation of Duchenne muscular dystrophy is rare due to X-chromosomal inheritance. We present two young girls with severe muscle weakness, muscular dystrophies, and creatine kinase (CK) levels exceeding 10,000 U/L. In the skeletal muscle tissues, dystrophin staining reaction showed mosaicism. The almost entirely skewed X-inactivation in both cases supported the possibility of a dystrophinopathy. Despite standard molecular diagnostics (including multiplex ligation-dependent probe amplification (MLPA) and next generation sequencing (NGS) gene panel sequencing), the genetic cause of the girls' conditions remained unknown. However, whole-genome sequencing revealed two reciprocal translocations between their X chromosomes and chromosome 5 and chromosome 19, respectively. In both cases, the breakpoints on the X chromosomes were located directly within the DMD gene (in introns 54 and 7, respectively) and were responsible for the patients' phenotypes. Additional techniques such as Sanger sequencing, conventional karyotyping and fluorescence in situ hybridization (FISH) confirmed the disruption of DMD gene in both patients through translocations. These findings underscore the importance of accurate clinical data combined with histopathological analysis in pinpointing the suspected underlying genetic disorder. Moreover, our study illustrates the viability of whole-genome sequencing as a time-saving and highly effective method for identifying genetic factors responsible for complex genetic constellations in Duchenne muscular dystrophy (DMD).
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Affiliation(s)
- Natalie Pluta
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Arpad von Moers
- Department of Pediatrics and Neuropediatrics, DRK Kliniken Berlin, 14050 Berlin, Germany
| | - Astrid Pechmann
- Department of Neuropediatrics and Muscle Disorders, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117 Berlin, Germany
| | - Hans-Hilmar Goebel
- Department of Neuropathology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117 Berlin, Germany
| | | | - Beat Wolf
- iCoSys, University of Applied Sciences Western Switzerland, 1700 Fribourg, Switzerland
| | - Indrajit Nanda
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Ann-Kathrin Zaum
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Simone Rost
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
- Medical Genetics Center (MGZ), 80335 Munich, Germany
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Uehara DT, Muramatsu T, Ishii S, Suzuki H, Fukushima K, Arasaki Y, Hayata T, Inazawa J, Ezura Y. Identification of a Biallelic Missense Variant in Gasdermin D (c.823G > C, p.Asp275His) in a Patient of Atypical Gorham-Stout Disease in a Consanguineous Family. JBMR Plus 2023; 7:e10784. [PMID: 37701150 PMCID: PMC10494506 DOI: 10.1002/jbm4.10784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/08/2023] [Accepted: 05/26/2023] [Indexed: 09/14/2023] Open
Abstract
Gorham-Stout disease (GSD), also called vanishing bone disease, is a rare osteolytic disease, frequently associated with lymphangiomatous tissue proliferation. The causative genetic background has not been noted except for a case with a somatic mutation in KRAS. However, in the present study, we encountered a case of GSD from a consanguineous family member. Whole-exome sequencing (WES) analysis focusing on rare recessive variants with zero homozygotes in population databases identified a homozygous missense variant (c.823G > C, p.Asp275His) in gasdermin D (GSDMD) in the patient and heterozygous in his unaffected brother. Because this variant affects the Asp275 residue that is involved in proteolytic cleavage by caspase-11 (as well as -4 and -5) to generate an activating p30 fragment required for pyroptotic cell death and proinflammation, we confirmed the absence of this cleavage product in peripheral monocytic fractions from the patient. A recent study indicated that a shorter p20 fragment, generated by further cleavage at Asp88, has a cell-autonomous function to suppress the maturation of osteoclasts to resorb bone matrix. Thus, the present study suggests for the first time the existence of hereditary GSD cases or novel GSD-like diseases caused by GSDMD deficiency. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Daniela Tiaki Uehara
- Department of Molecular CytogeneticsMedical Research Institute, Tokyo Medical and Dental University (TMDU)TokyoJapan
| | - Tomoki Muramatsu
- Department of Molecular CytogeneticsMedical Research Institute, Tokyo Medical and Dental University (TMDU)TokyoJapan
| | - Senichi Ishii
- Saku Central Hospital Advanced Care CenterSakuJapan
- Present address:
Ome Municipal General Hospital, OmeTokyoJapan
| | - Hidetsugu Suzuki
- Saku Central Hospital Advanced Care CenterSakuJapan
- Present address:
Department of Orthopedic SurgeryDokkyo Medical UniversitySaitamaJapan
| | | | - Yasuhiro Arasaki
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical SciencesTokyo University of ScienceChibaJapan
| | - Tadayoshi Hayata
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical SciencesTokyo University of ScienceChibaJapan
| | - Johji Inazawa
- Department of Molecular CytogeneticsMedical Research Institute, Tokyo Medical and Dental University (TMDU)TokyoJapan
- Research Core, TMDUTokyoJapan
| | - Yoichi Ezura
- Department of Joint Surgery and Sports MedicineTMDUTokyoJapan
- Department of Occupational Therapy, Faculty of Health and Medical ScienceTeikyo Heisei UniversityTokyoJapan
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5
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RNA-seq analysis, targeted long-read sequencing and in silico prediction to unravel pathogenic intronic events and complicated splicing abnormalities in dystrophinopathy. Hum Genet 2023; 142:59-71. [PMID: 36048237 DOI: 10.1007/s00439-022-02485-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/24/2022] [Indexed: 01/18/2023]
Abstract
Dystrophinopathy is caused by alterations in DMD. Approximately 1% of patients remain genetically undiagnosed, because intronic variations are not detected by standard methods. Here, we combined laboratory and in silico analyses to identify disease-causing genomic variants in genetically undiagnosed patients and determine the regulatory mechanisms underlying abnormal DMD transcript generation. DMD transcripts from 20 genetically undiagnosed dystrophinopathy patients in whom no exon variants were identified, despite dystrophin deficiency on muscle biopsy, were analyzed by transcriptome sequencing. Genome sequencing captured intronic variants and their effects were interpreted using in silico tools. Targeted long-read sequencing was applied in cases with suspected structural genomic abnormalities. Abnormal DMD transcripts were detected in 19 of 20 cases; Exonization of intronic sequences in 15 cases, exon skipping in one case, aberrantly spliced and polyadenylated transcripts in two cases and transcription termination in one case. Intronic single nucleotide variants, chromosomal rearrangements and nucleotide repeat expansion were identified in DMD gene as pathogenic causes of transcript alteration. Our combined analysis approach successfully identified pathogenic events. Detection of diseasing-causing mechanisms in DMD transcripts could inform the therapeutic options for patients with dystrophinopathy.
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Zaum AK, Nanda I, Kress W, Rost S. Detection of pericentric inversion with breakpoint in DMD by whole genome sequencing. Mol Genet Genomic Med 2022; 10:e2028. [PMID: 35912688 PMCID: PMC9544221 DOI: 10.1002/mgg3.2028] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/25/2022] [Accepted: 07/08/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Dystrophinopathies caused by variants in the DMD gene are a well-studied muscle disease. The most common type of variant in DMD are large deletions. Very rarely reported forms of variants are chromosomal translocations, inversions and deep intronic variants (DIVs) because they are not detectable by standard diagnostic techniques (sequencing of coding sequence, copy number variant detection). This might be the reason that some clinically and histologically proven dystrophinopathy cases remain unsolved. METHODS We used whole genome sequencing (WGS) to screen the entire DMD gene for variants in one of two brothers suffering from typical muscular dystrophy with strongly elevated creatine kinase levels. RESULTS Although a pathogenic DIV could not be detected, we were able to identify a pericentric inversion with breakpoints in DMD intron 44 and Xq13.3, which could be confirmed by Sanger sequencing in the index as well as in his brother and mother. As this variation affects a major part of DMD it is most likely disease causing. CONCLUSION Our findings elucidate that WGS is capable of detecting large structural rearrangements and might be suitable for the genetic diagnostics of dystrophinopathies in the future. In particular, inversions might be a more frequent cause for dystrophinopathies as anticipated and should be considered in genetically unsolved dystrophinopathy cases.
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Affiliation(s)
- Ann-Kathrin Zaum
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Indrajit Nanda
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Wolfram Kress
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Simone Rost
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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7
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Pasińska M, Łazarczyk E, Repczyńska A, Sobczyńska-Tomaszewska A, Zimowski J, Runge A, Haus O. Clinical Importance of aCGH in Genetic Counselling of Children with Psychomotor Retardation. Appl Clin Genet 2022; 15:27-38. [PMID: 35603035 PMCID: PMC9116409 DOI: 10.2147/tacg.s357136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/13/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction The X and Y chromosomes are responsible for the determination and differentiation of the gonads, and their numerical and structural abnormalities may cause the abnormal development of secondary sex characteristics. The presence of abnormalities concerning X chromosome can also contribute to many genetically heterogeneous diseases associated with cognitive impairment and intellectual disability. Purpose This study shows the effect of aberrations of the maternal X chromosome on the abnormal development of the child. Patients and Methods Ten women aged 26 to 40 years were consulted in genetic counselling clinic and subsequently subjected to cytogenetic and molecular tests due to abnormal psychomotor development of their children, in whom structural aberrations of the X chromosome had been detected. Results Two women were diagnosed with changes in karyotype: 46,X,der(X)t(X;Y)(p22.3;q11.2) in one and 46,X,inv(X)(p21.2q13). Five women were diagnosed with microduplications in the short arm of the X chromosome; dupXp22.31 in one, and in four women dupXp22.33. The remaining three women were diagnosed with duplication in the long arm of the X chromosome; dupXq25 in one and dupXq26.3 in two women. Conclusion Genetic analysis of the X chromosome, based on cytogenetic and molecular methods of the highest available resolution, is extremely important in women with reproductive failure. These methods allow establishing accurately the breakpoints and rearrangements in chromosomes, and assessment of the copy number variation (CNV) can explain phenotypic variability with apparently similar aberrations. A more precise characterization of the alterations is necessary for the correct genetic diagnosis, as well as determination of the carrier status and genetic risk in family members.
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Affiliation(s)
- Magdalena Pasińska
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Ewelina Łazarczyk
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Anna Repczyńska
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | | | - Janusz Zimowski
- Department of Genetics, Institute of Psychiatry and Neurology, Warszawa, Poland
| | - Agata Runge
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Olga Haus
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
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8
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Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene ( DMD). Int J Mol Sci 2021; 23:ijms23010059. [PMID: 35008485 PMCID: PMC8744749 DOI: 10.3390/ijms23010059] [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: 11/27/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
While in most patients the identification of genetic alterations causing dystrophinopathies is a relatively straightforward task, a significant number require genomic and transcriptomic approaches that go beyond a routine diagnostic set-up. In this work, we present a Becker Muscular Dystrophy patient with elevated creatinine kinase levels, progressive muscle weakness, mild intellectual disability and a muscle biopsy showing dystrophic features and irregular dystrophin labelling. Routine molecular techniques (Southern-blot analysis, multiplex PCR, MLPA and genomic DNA sequencing) failed to detect a defect in the DMD gene. Muscle DMD transcript analysis (RT-PCR and cDNA-MLPA) showed the absence of exons 75 to 79, seen to be present at the genomic level. These results prompted the application of low-coverage linked-read whole-genome sequencing (WGS), revealing a possible rearrangement involving DMD intron 74 and a region located upstream of the PRDX4 gene. Breakpoint PCR and Sanger sequencing confirmed the presence of a ~8 Mb genomic inversion. Aberrant DMD transcripts were subsequently identified, some of which contained segments from the region upstream of PRDX4. Besides expanding the mutational spectrum of the disorder, this study reinforces the importance of transcript analysis in the diagnosis of dystrophinopathies and shows how WGS has a legitimate role in clinical laboratory genetics.
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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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A Novel de Novo Paracentric Inversion [inv(20)(q13.1q13.3)] Accompanied by an 11q14.3-q21 Microdeletion in a Pediatric Patient with an Intellectual Disability. Balkan J Med Genet 2019; 21:63-67. [PMID: 30984528 PMCID: PMC6454239 DOI: 10.2478/bjmg-2018-0016] [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] [Indexed: 11/20/2022] Open
Abstract
A novel de novo paracentric inversion of the long arm of chromosome 20 [inv(20)(q13.1q13.3)], detected by conventional karyotyping in a 14-year-old boy with mental retardation is described. Further investigation by array comparative genomic hybridization (aCGH) revealed that the 20q inversion was not accompanied by microdeletions/microduplications containing disease-associated genes near or at the breakpoints. Two deletions at chromosomal regions 11q14.3q21 and 20q12 of 4.5 and 1.97 Mb size, respectively, containing important online Mendelian inheritance in man (OMIM) genes, were detected. The 4.5Mb 11q14.3q21 microdeletion was contained within a region that is involved, in most of the reported cases, with the interstitial 11q deletion and may be related to the mental retardation and developmental delay present in the patient. On the other hand, the published data about the 20q12 microdeletion are very few and it is not possible to correlate this finding with our patient’s phenotype. This case report contributes to the description of a new chromosomal entity, not previously reported, and is therefore important, especially in prenatal diagnosis and management of patients. Array comparative genomic hybridization has proven a useful technique for detecting submicroscopic rearrangements and should be offered prenatally, especially in cases of de novo karyotypically balanced chromosomal inversions or translocations in order to unveil other unbalanced chromosomal abnormalities such as deletions and amplifications.
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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: 37] [Impact Index Per Article: 5.3] [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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12
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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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13
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The Largest Paracentric Inversion, the Highest Rate of Recombinant Spermatozoa. Case Report: 46,XY, inv(2)(q21.2q37.3) and Literature Review. Balkan J Med Genet 2015; 17:55-62. [PMID: 25741216 PMCID: PMC4347478 DOI: 10.2478/bjmg-2014-0025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Carriers of inversions involving euchromatic regions are at risk of having unbalanced offspring due to meiotic crossover. In carriers, recombination can occur during gametogenesis and cause genetically unbalanced sperm and subsequently unbalanced embryos. Here we present segregation analysis results of an infertile male with 46,XY,inv(2) (q21.2q37.3) using fluorescent in situ hybridization (FISH) on sperm cells. This is the largest paracentric inversion (PAI) reported so far in a meiotic segregation analysis study. Sperm FISH revealed 28.0% recombinant spermatozoa rate for chromo-some 2, which was the highest rate in PAI carriers in the literature. Our results indicate a clear correlation between the size of the inverted segment and the frequency of the recombinant spermatozoa. The results of the FISH analysis with the information of unbalanced spermatozoa rate can provide accurate counseling on the genetic risk of infertility.
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14
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Atencia-Fernandez S, Shiel RE, Mooney CT, Nolan CM. Muscular dystrophy in the Japanese Spitz: an inversion disrupts the DMD and RPGR genes. Anim Genet 2015; 46:175-84. [PMID: 25644216 DOI: 10.1111/age.12266] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2014] [Indexed: 11/29/2022]
Abstract
An X-linked muscular dystrophy, with deficiency of full-length dystrophin and expression of a low molecular weight dystrophin-related protein, has been described in Japanese Spitz dogs. The aim of this study was to identify the causative mutation and develop a specific test to identify affected cases and carrier animals. Gene expression studies in skeletal muscle of an affected animal indicated aberrant expression of the Duchenne muscular dystrophy (dystrophin) gene and an anomaly in intron 19 of the gene. Genome-walking experiments revealed an inversion that interrupts two genes on the X chromosome, the Duchenne muscular dystrophy gene and the retinitis pigmentosa GTPase regulator gene. All clinically affected dogs and obligate carriers that were tested had the mutant chromosome, and it is concluded that the inversion is the causative mutation for X-linked muscular dystrophy in the Japanese Spitz breed. A PCR assay that amplifies mutant and wild-type alleles was developed and proved capable of identifying affected and carrier individuals. Unexpectedly, a 7-year-old male animal, which had not previously come to clinical attention, was shown to possess the mutant allele and to have a relatively mild form of the disease. This observation indicates phenotypic heterogeneity in Japanese Spitz muscular dystrophy, a feature described previously in humans and Golden Retrievers. With the availability of a simple, fast and accurate test for Japanese Spitz muscular dystrophy, detection of carrier animals and selected breeding should help eliminate the mutation from the breed.
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15
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Ołdak M, Ścieżyńska A, Młynarski W, Borowiec M, Ruszkowska E, Szulborski K, Pollak A, Kosińska J, Mueller-Malesińska M, Stawiński P, Szaflik JP, Płoski R. Evidence against RAB40AL being the locus for Martin-Probst X-linked deafness-intellectual disability syndrome. Hum Mutat 2014; 35:1171-4. [PMID: 25044830 DOI: 10.1002/humu.22620] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/02/2014] [Indexed: 11/06/2022]
Abstract
RAB40AL has been reported as the locus for Martin-Probst syndrome (MPS), an X-linked deafness-intellectual disability syndrome. The report was based on segregation of a missense change p.D59G with the disease in a single family and in vitro localization studies. We found the p.D59G variant by whole-exome sequencing in two patients; however, the diagnosis of MPS was excluded in both cases. Furthermore, screening of control DNA samples (n = 810) from a general Polish population, using allele-specific PCR and direct DNA sequencing for verification, identified p.D59G in 8/405 males and 12/405 females. High prevalence of the p.D59G variant (2.47%) is typical for a common genetic variation observed in asymptomatic individuals. Our data question the role of RAB40AL mutation as a disease-causing change and the involvement of RAB40AL in MPS. Considering an increasing use of next-generation sequencing in the clinical setting, our finding is of practical diagnostic importance.
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Affiliation(s)
- Monika Ołdak
- Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland; Institute of Physiology and Pathology of Hearing, Warsaw, Poland
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16
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Jiang JH, Gao Q, Shen XZ, Yu Y, Gu FM, Yan J, Pan JF, Jin F, Fan J, Zhou J, Huang XW. An X-chromosomal association study identifies a susceptibility locus at Xq22.1 for hepatitis B virus-related hepatocellular carcinoma. Clin Res Hepatol Gastroenterol 2013; 37:586-95. [PMID: 24209690 DOI: 10.1016/j.clinre.2013.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/01/2013] [Accepted: 09/17/2013] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND OBJECTIVE Genetic epidemiological data in hepatocellular carcinoma (HCC) pedigrees indicate a pattern of X-linked recessive inheritance of HCC susceptibility genes. This study is designed to test the hypothesis that there are genes conferring susceptibility to HCC located on the X-chromosome. METHODS An X-chromosomal association study was conducted among Chinese men recruited from an area with a high prevalence of HCC. The candidate gene was further investigated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). RESULTS By analyzing 5454 X-chromosome single nucleotide polymorphisms (SNPs) in 50 HCC patients and 50 controls, we found two promising regions in which the associated SNPs clustered, located at Xq22.1 and Xq26.2. We further selected 35 tag SNPs (tSNPs) from these two regions for additional genotyping analysis in another independent set of 290 cases and 242 controls. Notably, SNP rs5945919 at Xq22.1 exhibited a significant association with HBV-related HCC (odds ratio [OR]=2.22, 95% confidence interval [CI]=1.15-4.30, P=0.016). The expressions of the three genes near the rs5945919 locus, RAB40AL, BEX1, and NXF3, were analyzed by qRT-PCR between another 24 HCC tissues and paired peritumoral liver tissues. The results indicated that NXF3, rather than RAB40AL and BEX1, mRNA level was found to be more abundant in HCC tissue than in peritumoral liver tissue. CONCLUSIONS Our findings implicated Xq22.1 as a novel susceptibility locus for HCC and NXF3 as a candidate risk factor for relevant HCC.
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Affiliation(s)
- Jia-Hao Jiang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, P.R. China
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17
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Thu Tran TH, Zhang Z, Yagi M, Lee T, Awano H, Nishida A, Okinaga T, Takeshima Y, Matsuo M. Molecular characterization of an X(p21.2;q28) chromosomal inversion in a Duchenne muscular dystrophy patient with mental retardation reveals a novel long non-coding gene on Xq28. J Hum Genet 2012; 58:33-9. [DOI: 10.1038/jhg.2012.131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Bedoyan JK, Schaibley VM, Peng W, Bai Y, Mondal K, Shetty AC, Durham M, Micucci JA, Dhiraaj A, Skidmore JM, Kaplan JB, Skinner C, Schwartz CE, Antonellis A, Zwick ME, Cavalcoli JD, Li JZ, Martin DM. Disruption of RAB40AL function leads to Martin--Probst syndrome, a rare X-linked multisystem neurodevelopmental human disorder. J Med Genet 2012; 49:332-40. [PMID: 22581972 PMCID: PMC3350147 DOI: 10.1136/jmedgenet-2011-100575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND AND AIM Martin--Probst syndrome (MPS) is a rare X-linked disorder characterised by deafness, cognitive impairment, short stature and distinct craniofacial dysmorphisms, among other features. The authors sought to identify the causative mutation for MPS. METHODS AND RESULTS Massively parallel sequencing in two affected, related male subjects with MPS identified a RAB40AL (also called RLGP) missense mutation (chrX:102,079,078-102,079,079AC→GA p.D59G; hg18). RAB40AL encodes a small Ras-like GTPase protein with one suppressor of cytokine signalling box. The p.D59G variant is located in a highly conserved region of the GTPase domain between β-2 and β-3 strands. Using RT-PCR, the authors show that RAB40AL is expressed in human fetal and adult brain and kidney, and adult lung, heart, liver and skeletal muscle. RAB40AL appears to be a primate innovation, with no orthologues found in mouse, Xenopus or zebrafish. Western analysis and fluorescence microscopy of GFP-tagged RAB40AL constructs from transiently transfected COS7 cells show that the D59G missense change renders RAB40AL unstable and disrupts its cytoplasmic localisation. CONCLUSIONS This is the first study to show that mutation of RAB40AL is associated with a human disorder. Identification of RAB40AL as the gene mutated in MPS allows for further investigations into the molecular mechanism(s) of RAB40AL and its roles in diverse processes such as cognition, hearing and skeletal development.
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Kawashima H, Watanabe K, Morishima Y, Ioi H, Kashiwagi Y, Miyajima T, Takekuma K, Nishino I, Numabe H. High concentration of middle chain fatty acid in a case of Duchenne muscular dystrophy with severe mental retardation. Pediatr Int 2012; 54:137-40. [PMID: 22335324 DOI: 10.1111/j.1442-200x.2011.03401.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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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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21
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Boone PM, Wiszniewski W, Lupski JR. Genomic medicine and neurological disease. Hum Genet 2011; 130:103-21. [PMID: 21594611 PMCID: PMC3133694 DOI: 10.1007/s00439-011-1001-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 04/27/2011] [Indexed: 12/11/2022]
Abstract
"Genomic medicine" refers to the diagnosis, optimized management, and treatment of disease--as well as screening, counseling, and disease gene identification--in the context of information provided by an individual patient's personal genome. Genomic medicine, to some extent synonymous with "personalized medicine," has been made possible by recent advances in genome technologies. Genomic medicine represents a new approach to health care and disease management that attempts to optimize the care of a patient based upon information gleaned from his or her personal genome sequence. In this review, we describe recent progress in genomic medicine as it relates to neurological disease. Many neurological disorders either segregate as Mendelian phenotypes or occur sporadically in association with a new mutation in a single gene. Heritability also contributes to other neurological conditions that appear to exhibit more complex genetics. In addition to discussing current knowledge in this field, we offer suggestions for maximizing the utility of genomic information in clinical practice as the field of genomic medicine unfolds.
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Affiliation(s)
- Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Bosch N, Morell M, Ponsa I, Mercader JM, Armengol L, Estivill X. Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism. PLoS One 2009; 4:e8269. [PMID: 20011547 PMCID: PMC2790694 DOI: 10.1371/journal.pone.0008269] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 11/12/2009] [Indexed: 12/12/2022] Open
Abstract
Background The human chromosome 8p23.1 region contains a 3.8–4.5 Mb segment which can be found in different orientations (defined as genomic inversion) among individuals. The identification of single nucleotide polymorphisms (SNPs) tightly linked to the genomic orientation of a given region should be useful to indirectly evaluate the genotypes of large genomic orientations in the individuals. Results We have identified 16 SNPs, which are in linkage disequilibrium (LD) with the 8p23.1 inversion as detected by fluorescent in situ hybridization (FISH). The variability of the 8p23.1 orientation in 150 HapMap samples was predicted using this set of SNPs and was verified by FISH in a subset of samples. Four genes (NEIL2, MSRA, CTSB and BLK) were found differentially expressed (p<0.0005) according to the orientation of the 8p23.1 region. Finally, we have found variable levels of mosaicism for the orientation of the 8p23.1 as determined by FISH. Conclusion By means of dense SNP genotyping of the region, haplotype-based computational analyses and FISH experiments we could infer and verify the orientation status of alleles in the 8p23.1 region by detecting two short haplotype stretches at both ends of the inverted region, which are likely the relic of the chromosome in which the original inversion occurred. Moreover, an impact of 8p23.1 inversion on gene expression levels cannot be ruled out, since four genes from this region have statistically significant different expression levels depending on the inversion status. FISH results in lymphoblastoid cell lines suggest the presence of mosaicism regarding the 8p23.1 inversion.
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Affiliation(s)
- Nina Bosch
- Genetic Causes of Disease Group, Genes and Disease Programme Center for Genomic Regulation (CRG-UPF), Barcelona, Catalonia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain
| | - Marta Morell
- Genetic Causes of Disease Group, Genes and Disease Programme Center for Genomic Regulation (CRG-UPF), Barcelona, Catalonia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain
| | - Immaculada Ponsa
- Genetic Causes of Disease Group, Genes and Disease Programme Center for Genomic Regulation (CRG-UPF), Barcelona, Catalonia, Spain
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Catalonia, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Josep Maria Mercader
- Genetic Causes of Disease Group, Genes and Disease Programme Center for Genomic Regulation (CRG-UPF), Barcelona, Catalonia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain
| | - Lluís Armengol
- Genetic Causes of Disease Group, Genes and Disease Programme Center for Genomic Regulation (CRG-UPF), Barcelona, Catalonia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain
- Quantitative Genomic Medicine Laboratories (qGenomics), Barcelona, Catalonia, Spain
| | - Xavier Estivill
- Genetic Causes of Disease Group, Genes and Disease Programme Center for Genomic Regulation (CRG-UPF), Barcelona, Catalonia, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain
- Department of Health and Experimental Life Sciences, Pompeu Fabra University (UPF), Barcelona, Catalonia, Spain
- * E-mail:
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Lawson MJ, Zhang L. Sexy gene conversions: locating gene conversions on the X-chromosome. Nucleic Acids Res 2009; 37:4570-9. [PMID: 19487239 PMCID: PMC2724270 DOI: 10.1093/nar/gkp421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus) and rat (Rattus norvegicus) for evidence of gene conversion. We identified seven gene families (WD repeat protein family, Ferritin Heavy Chain family, RAS-related Protein RAB-40 family, Diphosphoinositol polyphosphate phosphohydrolase family, Transcription Elongation Factor A family, LDOC1-related family, Zinc Finger Protein ZIC, and GLI family) that show evidence of gene conversion. Through phylogenetic analyses and synteny evidence, we show that gene conversion has played an important role in the evolution of these gene families and that gene conversion has occurred independently in both primates and rodents. Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions. The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.
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24
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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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25
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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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Thomas NS, Bryant V, Maloney V, Cockwell AE, Jacobs PA. Investigation of the origins of human autosomal inversions. Hum Genet 2008; 123:607-16. [PMID: 18470537 DOI: 10.1007/s00439-008-0510-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 05/01/2008] [Indexed: 11/26/2022]
Abstract
A significant proportion of both pericentric and paracentric inversions have recurrent breakpoints and so could either have arisen through multiple independent events or be identical by descent (IBD) with a single common ancestor. Of two common variant inversions previously studied, the inv(2)(p11q13) was genuinely recurrent while the inv(10)(p11.2q21.2) was IBD in all cases tested. Excluding these two variants we have ascertained 257 autosomal inversion probands at the Wessex Regional Genetics Laboratory. There were 104 apparently recurrent inversions, representing 35 different breakpoint combinations and we speculated that at least some of these had arisen on more than one occasion. However, haplotype analysis identified no recurrent cases among eight inversions tested, including the variant inv(5)(p13q13). The cases not IBD were shown to have different breakpoints at the molecular cytogenetic level. No crossing over was detected within any of the inversions and the founder haplotypes extended for variable distances beyond the inversion breakpoints. Defining breakpoint intervals by FISH mapping identified no obvious predisposing elements in the DNA sequence. In summary the vast majority of human inversions arise as unique events. Even apparently recurrent inversions, with the exception of the inv(2)(p12q13), are likely to be either derived from a common ancestor or to have subtly different breakpoints. Presumably the lack of selection against most inversions allows them to accumulate and disperse amongst different populations over time.
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Affiliation(s)
- N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury SP2 8BJ, UK.
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27
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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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28
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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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29
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Hayashi S, Kurosawa K, Imoto I, Mizutani S, Inazawa J. Detection of cryptic chromosome aberrations in a patient with a balanced t(1;9)(p34.2;p24) by array-based comparative genomic hybridization. Am J Med Genet A 2006; 139:32-6. [PMID: 16222686 DOI: 10.1002/ajmg.a.30982] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Mental retardation (MR) is one of the most common phenotypes in congenital disorders, but in many cases the pathogenesis remains unknown. Here, we report on a 5-year-old boy with mild developmental disability, cranial malformation, minor anomalies, and moderate MR. G-banded chromosome analysis revealed that he carried an apparent balanced translocation, t(1;9)(p34.2;p24). However, our array-based comparative genomic hybridization (CGH-array) analysis detected a cryptic genomic duplication and a deletion at the breakpoints. Further fluorescence in situ hybridization (FISH) showed that the duplication was approximately 7.9 Mb in size at 1p34.3-p33, and the deletion was 4 Mb at 9pter-p24. Although some features of the patient were consistent with those of monosomy 9p-syndrome, his features were not typical of cases of the syndrome, suggesting that the small deletion region involved in 9p may limit his phenotype. On the other hand, interstitial duplication at 1p34.3-p33 is very rare and his phenotype did not match with that in previous reports. CGH-array is a potentially useful technique for investigating cryptic copy-number alterations in cases of apparently balanced chromosome rearrangements in patients with unexpected clinical features.
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MESH Headings
- Abnormalities, Multiple/genetics
- Child, Preschool
- Chromosome Aberrations
- Chromosome Deletion
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 9
- Gene Duplication
- Humans
- In Situ Hybridization, Fluorescence
- Intellectual Disability/genetics
- Male
- Nucleic Acid Hybridization/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, Tokyo, Japan
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30
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Gilling M, Dullinger JS, Gesk S, Metzke-Heidemann S, Siebert R, Meyer T, Brondum-Nielsen K, Tommerup N, Ropers HH, Tümer Z, Kalscheuer VM, Thomas NS. Breakpoint cloning and haplotype analysis indicate a single origin of the common Inv(10)(p11.2q21.2) mutation among northern Europeans. Am J Hum Genet 2006; 78:878-883. [PMID: 16642442 PMCID: PMC1474032 DOI: 10.1086/503632] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Accepted: 02/22/2006] [Indexed: 11/03/2022] Open
Abstract
The pericentric inv(10)(p11.2q21.2) mutation has been frequently identified in cytogenetic laboratories, is phenotypically silent, and is considered to be a polymorphic variant. Cloning and sequencing of the junction fragments on 10p11 and 10q21 revealed that neither inversion breakpoint directly involved any genes or repetitive sequences, although both breakpoint regions contain a number of repeats. All 20 apparently unrelated inv(10) families in our study had identical breakpoints, and detailed haplotype analysis showed that the inversions were identical by descent. Thus, although considered a common variant, inv(10)(p11.2q21.2) has a single ancestral founder among northern Europeans.
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Affiliation(s)
- Mette Gilling
- Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen, Copenhagen
| | - Jörn S Dullinger
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Charité University Hospital, Berlin, Germany
| | - Stefan Gesk
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Simone Metzke-Heidemann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | | | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen, Copenhagen
| | | | - Zeynep Tümer
- Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen, Copenhagen
| | | | - N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, United Kingdom.
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31
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Nishioka K, Hayashi S, Farrer MJ, Singleton AB, Yoshino H, Imai H, Kitami T, Sato K, Kuroda R, Tomiyama H, Mizoguchi K, Murata M, Toda T, Imoto I, Inazawa J, Mizuno Y, Hattori N. Clinical heterogeneity of alpha-synuclein gene duplication in Parkinson's disease. Ann Neurol 2006; 59:298-309. [PMID: 16358335 DOI: 10.1002/ana.20753] [Citation(s) in RCA: 218] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE Recently, genomic multiplications of alpha-synuclein gene (SNCA) have been reported to cause hereditary early-onset parkinsonism. The objective of this study was to assess the frequency of SNCA multiplications among autosomal dominant hereditary Parkinson's disease (ADPD). METHODS We screened 113 ADPD probands and 200 sporadic PD cases by quantitative polymerase chain reaction and confirmed SNCA multiplications by fluorescence in situ hybridization (FISH) and comparative genomic hybridization array. RESULTS Two families (two patients from Family A and one from Family B) with SNCA duplication were identified among ADPD patients. Even though they had the same SNCA duplication, one patient had dementia. Because there was exactly the same difference between the regions originated from each patient, the finding suggests that the phenotype of SNCA multiplication may be also influenced by the range of duplication region. We also detected asymptomatic carriers in the families of both patients. Interestingly, the penetrance ratio was 33.3% (2/6) in one kindred, indicating that the ratio was very much lower than expected. INTERPRETATION These two newly identified Japanese patients with SNCA duplication and the five previously identified American and European families with SNCA triplication or duplication mutations indicate that the incidence of SNCA multiplication may be more frequent than previously estimated.
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Affiliation(s)
- Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
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Bhat SS, Schmidt KR, Ladd S, Kim KC, Schwartz CE, Simensen RJ, DuPont BR, Stevenson RE, Srivastava AK. Disruption of DMD and deletion of ACSL4 causing developmental delay, hypotonia, and multiple congenital anomalies. Cytogenet Genome Res 2006; 112:170-5. [PMID: 16276108 DOI: 10.1159/000087531] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Accepted: 03/07/2005] [Indexed: 01/06/2023] Open
Abstract
We have studied a male patient with significant developmental delay, growth failure, hypotonia, girdle weakness, microcephaly, and multiple congenital anomalies including atrial (ASD) and ventricular (VSD) septal defects. Detailed cytogenetic and molecular analyses revealed three de novo X chromosome aberrations and a karyotype 46,Y,der(X)inv(X) (p11.4q11.2)inv(X)(q11.2q21.32 approximately q22.2)del(X)(q22.3q22.3) was determined. The three X chromosome aberrations in the patient include: a pericentric inversion (inv 1) that disrupted the Duchenne muscular dystrophy (DMD) gene, dystrophin, at Xp11.4; an Xq11.2q21.32 approximately q22.2 paracentric inversion (inv 2) putatively affecting no genes; and an interstitial deletion at Xq22.3 that results in functional nullisomy of several known genes, including a gene previously associated with X-linked nonsyndromic mental retardation, acyl-CoA synthetase long chain family member 4 (ACSL4). These findings suggest that the disruption of DMD and the absence of ACSL4 in the patient are responsible for neuromuscular disease and cognitive impairment.
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Affiliation(s)
- S S Bhat
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC, USA
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33
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Anton E, Blanco J, Egozcue J, Vidal F. Sperm studies in heterozygote inversion carriers: a review. Cytogenet Genome Res 2005; 111:297-304. [PMID: 16192708 DOI: 10.1159/000086903] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Accepted: 02/22/2005] [Indexed: 01/31/2023] Open
Abstract
The risk of producing unbalanced gametes in heterozygous inversion carriers mostly depends on the occurrence of recombination events within the inverted segment. Recombination determines the possibility of producing chromosomes with duplications/deficiencies (pericentric inversions) or with duplications/deficiencies which furthermore appear as dicentric and acentric fragments (paracentric inversions). In this work, a general description of the close relationship between the occurrence of crossovers in pericentric and paracentric inversions and the final segregation outcome is presented. After this introduction, a compilation of inversion segregation data and interchromosomal effect results from previously published sperm studies have been reviewed. Segregation results indicate a great heterogeneity in the percentage of unbalanced gametes, from 0 to 37.38%. The size of the inverted segments and their proportion in the chromosome are two parameters closely related with the incidence of recombination (P < 0.0001; using a quadratic model and Pearson's correlation test). These results suggest that the production of a significant level of unbalanced gametes would require a minimum inversion size of 100 Mbp and the inversion of at least 50% of the chromosome. Interchromosomal effects are seldom observed in chromosomal inversions. Finally, implications of the meiotic behavior of the inversions in the progeny of the carriers and the incorporation of sperm FISH segregation analysis for reproductive genetic counseling are discussed.
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Affiliation(s)
- E Anton
- Unitat de Biologia Cellular, Universitat Autònoma de Barcelona, Barcelona, Spain
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Struys T, Krage T, Vandenabeele F, Raab WHM, Lambrichts I. Immunohistochemical evidence for proteolipid protein and nestin expression in the late bell stage of developing rodent teeth. Arch Oral Biol 2005; 50:171-4. [PMID: 15721146 DOI: 10.1016/j.archoralbio.2004.11.007] [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: 09/09/2004] [Accepted: 11/02/2004] [Indexed: 11/20/2022]
Abstract
In this study, the expression of proteolipid protein (PLP) and nestin is studied in the late bell stage of developing rodent teeth in neonatal rats. By using immunohistochemistry, it was shown that odontoblasts, ameloblasts and the stratum intermedium are positive for PLP in regions of active matrix deposition. Reactivity for nestin could be detected in the odontoblasts, stratum intermedium and in some of the apical processes of the ameloblasts. The fact that mutations in the PLP gene can cause disturbances in tooth form, number and eruption taken together with the presence of PLP reactivity in odontoblasts and ameloblasts of healthy animals, suggests a crucial role for PLP in developing teeth because of its structural supportive characteristics. These results also imply the possible use of PLP antibody as a new marker for, respectively, dentin and enamel-secreting odontoblasts and ameloblasts. PLP and nestin expression could point to a possible similarity in function between the oligodendrocyte and the odontoblast, both derived from the neural crest. To compare with the situation in human tissue, PLP and nestin expression were preliminarily tested on human dental pulp. The odontoblasts were positive for both PLP and nestin.
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Affiliation(s)
- T Struys
- Limburgs Universitair Centrum, Biomedisch Onderzoeksinstituut and Transnationale Universiteit Limburg, School for Life Sciences, Diepenbeek, Belgium.
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Inoue K. PLP1-related inherited dysmyelinating disorders: Pelizaeus-Merzbacher disease and spastic paraplegia type 2. Neurogenetics 2004; 6:1-16. [PMID: 15627202 DOI: 10.1007/s10048-004-0207-y] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Accepted: 11/17/2004] [Indexed: 10/26/2022]
Abstract
Pelizaeus-Merzbacher disease (PMD) and its allelic disorder, spastic paraplegia type 2 (SPG2), are among the best-characterized dysmyelinating leukodystrophies of the central nervous system (CNS). Both PMD and SPG2 are caused by mutations in the proteolipid protein 1 (PLP1) gene, which encodes a major component of CNS myelin proteins. Distinct types of mutations, including point mutations and genomic duplications and deletions, have been identified as causes of PMD/SPG2 that act through different molecular mechanisms. Studies of various PLP1 mutants in humans and animal models have shed light on the genomic, molecular, and cellular pathogeneses of PMD/SPG2. Recent discoveries include complex mutational mechanisms and associated disease phenotypes, novel cellular pathways that lead to the degeneration of oligodendrocytes, and genomic architectural features that result in unique chromosomal rearrangements. Here, I review the previous and current knowledge of the molecular pathogenesis of PMD/SPG2 and delineate future directions for PMD/SPG2 studies.
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Affiliation(s)
- Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8502, Japan.
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Abstract
Muscular dystrophies are a heterogeneous group of inherited disorders characterized by progressive muscle wasting and weakness. Majority of genes and their protein products responsible for the dystrophies have been identified in recent years. Using molecular studies, now it is possible to establish a precise diagnosis, provide prognosis, detect preclinical cases, identify carriers, and offer prenatal diagnostic testing. Molecular genetic approaches also seem to offer the best prospect for developing effective treatments in the future.
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Affiliation(s)
- Monisha Mukherjee
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, India
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