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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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Misra S, Peters G, Barnes E, Ardern-Holmes S, Webster R, Troedson C, Mohammad SS, Gill D, Menezes M, Gupta S, Procopis P, Antony J, Kurian MA, Dale RC. Yield of comparative genomic hybridization microarray in pediatric neurology practice. NEUROLOGY-GENETICS 2019; 5:e367. [PMID: 31872051 PMCID: PMC6878849 DOI: 10.1212/nxg.0000000000000367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/28/2019] [Indexed: 12/14/2022]
Abstract
Objective The present study investigated the diagnostic yield of array comparative genomic hybridization (aCGH) in a large cohort of children with diverse neurologic disorders as seen in child neurology practice to test whether pathogenic copy number variants (CNVs) were more likely to be detected in specific neurologic phenotypes. Methods A retrospective cross-sectional analysis was performed on 555 children in whom a genetic etiology was suspected and who underwent whole-genome aCGH testing between 2006 and 2012. Neurologic phenotyping was performed using hospital medical records. An assessment of pathogenicity was made for each CNV, based on recent developments in the literature. Results Forty-seven patients were found to carry a pathogenic CNV, giving an overall diagnostic yield of 8.59%. Certain phenotypes predicted for the presence of a pathogenic CNV, including developmental delay (odds ratio [OR] 3.69 [1.30-10.51]), cortical visual impairment (OR 2.73 [1.18-6.28]), dysmorphism (OR 2.75 [1.38-5.50]), and microcephaly (OR 2.16 [1.01-4.61]). The combination of developmental delay/intellectual disability with dysmorphism and abnormal head circumference was also predictive for a pathogenic CNV (OR 2.86 [1.02-8.00]). For every additional clinical feature, there was an increased likelihood of detecting a pathogenic CNV (OR 1.18 [1.01-1.38]). Conclusions The use of aCGH led to a pathogenic finding in 8.59% of patients. The results support the use of aCGH as a first tier investigation in children with diverse neurologic disorders, although whole-genome sequencing may replace aCGH as the detection method in the future. In particular, the yield was increased in children with developmental delay, dysmorphism, cortical visual impairment, and microcephaly.
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Affiliation(s)
- Shibalik Misra
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Greg Peters
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Elizabeth Barnes
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Simone Ardern-Holmes
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Richard Webster
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Christopher Troedson
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Shekeeb S Mohammad
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Deepak Gill
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Manoj Menezes
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Sachin Gupta
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Peter Procopis
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Jayne Antony
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Manju A Kurian
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Russell C Dale
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
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Lee CL, Lee CH, Chuang CK, Chiu HC, Chen YJ, Chou CL, Wu PS, Chen CP, Lin HY, Lin SP. Array-CGH increased the diagnostic rate of developmental delay or intellectual disability in Taiwan. Pediatr Neonatol 2019; 60:453-460. [PMID: 30581099 DOI: 10.1016/j.pedneo.2018.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 10/03/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Unexplained developmental delay or intellectual disability (DD/ID) has an estimated prevalence of about 3%-5% in the general population of Taiwan. Array comparative genomic hybridization (array-CGH) is a high-resolution tool that can detect about 50 Kb chromosome aberrations. A previous study has reported a detection rate of 10%-20% for this array.1 This study aimed to investigate and compare the diagnosis rate for DD/ID using array-CGH and conventional chromosome study in DD/ID patients in Taiwan. METHODS We enrolled 177 patients with DD/ID who underwent array-CGH examination at the MacKay Memory Hospital between June 2010 and September 2017. The copy number variants (CNV) were classified into the following three groups: pathogenic (potential pathologic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance, VOUS), according to the ACMG guideline.2 RESULTS: Of the 177 enrolled patients, 100 (56.5%) were men and 77 (43.5%) were women. Ages ranged from 3 months to 50 years, with a median age of 5.2 years. Total 32.0% (32/100) male patients had pathogenic CNV, and 32.5% (25/77) female patients had pathogenic CNV. The ratio of pathogenic CNV in male and female patients was not significantly different (p = 0.379). The proportions of pathogenic CNV at <3 years, 3-6 years, 6-12 years, 12-18 years, and >18 years of age were 32.3% (31/96), 19.4% (6/31), 34.8% (8/23), 16.7% (2/12), and 66.7% (10/15), respectively. The overall diagnosed rate of DD/ID with pathogenic CNV was 27.7% (49/177) using array-CGH in this study. There were 105 patients with conventional karyotyping and array-CGH data at the same time. Nineteen (18.1%) patients had visible chromosomal abnormality. Total 32/105 (30.5%) patients could find at least one pathogenic CNVs. The array-CGH had a higher diagnosed rate than the conventional karyotyping in clinical application. CONCLUSIONS Although array-CGH could not detect point mutation, balanced translocations, inversions, or low-level mosaicism, the diagnosis rate in clinical application was up to 46.3% and 2.5 times that of conventional karyotyping analysis (18.1%). This study demonstrated that array-CGH is a powerful diagnostic tool and should be the first genetic test instead of conventional karyotyping analysis for patients with unexplained DD/ID.
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Affiliation(s)
- Chung-Lin Lee
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chen-Hao Lee
- Department of Pediatrics, E-DA Hospital, I-Shou University, Kaohsiung City, Taiwan
| | | | - Huei-Ching Chiu
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yen-Jiun Chen
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chao-Ling Chou
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | | | - Chih-Ping Chen
- Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Departments of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hsiang-Yu Lin
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan; Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan; Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan.
| | - Shuan-Pei Lin
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan; Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan.
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Array comparative genomic hybridization and genomic sequencing in the diagnostics of the causes of congenital anomalies. J Appl Genet 2016; 58:185-198. [PMID: 27858254 DOI: 10.1007/s13353-016-0376-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/19/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
The aim of this review is to provide the current state of knowledge about the usefulness of modern genetic technologies in uncovering the causality of isolated and multiple congenital anomalies. Array comparative genomic hybridization and next-generation sequencing have revolutionized the clinical approach to patients with these phenotypes. Both technologies enable early diagnosis, especially in clinically challenging newborn populations, and help to uncover genetic defects associated with various phenotypes. The application of both complementary methods could assist in identifying many variants that may simultaneously be involved in the development of a number of isolated or multiple congenital anomalies. Both technologies carry serious variant misinterpretation risks as well. Therefore, the methods of variant classification and accessible variant databases are mentioned. A useful strategy of clinical genetic testing with the application of both methodologies is presented. Finally, future directions and challenges are briefly commented on in this review.
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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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Uehara DT, Hayashi S, Okamoto N, Mizuno S, Chinen Y, Kosaki R, Kosho T, Kurosawa K, Matsumoto H, Mitsubuchi H, Numabe H, Saitoh S, Makita Y, Hata A, Imoto I, Inazawa J. SNP array screening of cryptic genomic imbalances in 450 Japanese subjects with intellectual disability and multiple congenital anomalies previously negative for large rearrangements. J Hum Genet 2016; 61:335-43. [PMID: 26740234 DOI: 10.1038/jhg.2015.154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/30/2015] [Accepted: 11/20/2015] [Indexed: 11/09/2022]
Abstract
Intellectual disability (ID) is a heterogeneous condition affecting 2-3% of the population, often associated with multiple congenital anomalies (MCA). The genetic cause remains largely unexplained for most cases. To investigate the causes of ID/MCA of unknown etiology in the Japanese population, 645 subjects have been recruited for the screening of pathogenic copy-number variants (CNVs). Two screenings using bacterial artificial chromosome (BAC) arrays were previously performed, which identified pathogenic CNVs in 133 cases (20.6%; Hayashi et al., J. Hum. Genet., 2011). Here, we present the findings of the third screening using a single-nucleotide polymorphism (SNP) array, performed in 450 negative cases from our previous report. Pathogenic CNVs were found in 22 subjects (4.9%), in which 19 CNVs were located in regions where clinical significance had been previously established. Among the 22 cases, we identified PPFIA2 as a novel candidate gene for ID. Analysis of copy-neutral loss of heterozygosity (CNLOH) detected one case in which the CNLOH regions seem to be significant. The SNP array detected a modest fraction of small causative CNVs, which is explained by the fact that the majority of causative CNVs have larger sizes, and those had been mostly identified in the two previous screenings.
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Affiliation(s)
- Daniela Tiaki Uehara
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shin Hayashi
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Kasugai, Japan
| | - Yasutsugu Chinen
- Department of Pediatrics, Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Hiroshi Mitsubuchi
- Department of Pediatrics, Kumamoto University Graduate School of Medical Science, Kumamoto, Japan
| | - Hironao Numabe
- Department of Genetic Counseling, Faculty of Core Research, Ochanomizu University, Tokyo, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa, Japan
| | - Akira Hata
- Department of Public Health, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Issei Imoto
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
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Hayashi S, Yagi M, Morisaki I, Inazawa J. Identical deletion at 14q13.3 including PAX9 and NKX2-1 in siblings from mosaicism of unaffected parent. J Hum Genet 2015; 60:203-6. [DOI: 10.1038/jhg.2014.123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 01/19/2023]
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Matsumoto H, Zaha K, Nakamura Y, Hayashi S, Inazawa J, Nonoyama S. Chromosome 9q33q34 microdeletion with early infantile epileptic encephalopathy, severe dystonia, abnormal eye movements, and nephroureteral malformations. Pediatr Neurol 2014; 51:170-5. [PMID: 24938147 DOI: 10.1016/j.pediatrneurol.2014.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 03/10/2014] [Accepted: 03/15/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND Microdeletion of chromosome 9q33q34 is an emerging disease disorder associated with early infantile epileptic encephalopathy, intellectual disability, and a variety of movement disorders. PATIENT We describe a male infant with early infantile epileptic encephalopathy with suppression-burst (Ohtahara syndrome) who carried a de novo 2.0-Mb microdeletion in chromosome 9q33q34, including STXBP1. The previously reported examples of 9q33q34 microdeletion including STXBP1 are reviewed. RESULTS The patient developed infantile spasms at 4 months of age, and these were refractory to multiple antiepileptic drugs. He also developed severe dystonia during infancy, rotatory nystagmus, and nephroureteral malformations. Immunoglobulin and clobazam administered at 11 months were effective for the spasms, but profound psychomotor retardation remained. A comparative genomic hybridization array analysis and the fluorescence in situ hybridization analysis revealed a de novo 2.0-Mb microdeletion in chromosome 9q33q34, which encompasses STXBP1, ENG, SPTAN1, and 52 other genes. A total of 14 patients (13 from the literature) with a 9q33q24 microdeletion including STXBP1 were reviewed, five of them displayed early infantile epileptic encephalopathy with suppression-burst, and six of them had early-onset epilepsy but not early infantile epileptic encephalopathy. Dystonia has been previously described in 9q33q34 deletions involving TOR1A but not STXBP1. Neither abnormal eye movements nor nephroureteral malformations has been previously described. CONCLUSIONS This patient adds unique clinical presentations of neurological and nephroureteral abnormalities to the features of 9q33q34 microdeletion.
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Affiliation(s)
- Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan.
| | - Kiyotaka Zaha
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan
| | - Yasuko Nakamura
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan
| | - Shin Hayashi
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan
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Hooli BV, Kovacs-Vajna ZM, Mullin K, Blumenthal MA, Mattheisen M, Zhang C, Lange C, Mohapatra G, Bertram L, Tanzi RE. Rare autosomal copy number variations in early-onset familial Alzheimer's disease. Mol Psychiatry 2014; 19:676-81. [PMID: 23752245 DOI: 10.1038/mp.2013.77] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/19/2013] [Accepted: 04/15/2013] [Indexed: 01/08/2023]
Abstract
Over 200 rare and fully penetrant pathogenic mutations in amyloid precursor protein (APP), presenilin 1 and 2 (PSEN1 and PSEN2) cause a subset of early-onset familial Alzheimer's disease (EO-FAD). Of these, 21 cases of EO-FAD families carrying unique APP locus duplications remain the only pathogenic copy number variations (CNVs) identified to date in Alzheimer's disease (AD). Using high-density DNA microarrays, we performed a comprehensive genome-wide analysis for the presence of rare CNVs in 261 EO-FAD and early/mixed-onset pedigrees. Our analysis revealed 10 novel private CNVs in 10 EO-FAD families overlapping a set of genes that includes: A2BP1, ABAT, CDH2, CRMP1, DMRT1, EPHA5, EPHA6, ERMP1, EVC, EVC2, FLJ35024 and VLDLR. In addition, CNVs encompassing two known frontotemporal dementia genes, CHMP2B and MAPT were found. To our knowledge, this is the first study reporting rare gene-rich CNVs in EO-FAD and early/mixed-onset AD that are likely to underlie pathogenicity in familial AD and perhaps related dementias.
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Affiliation(s)
- B V Hooli
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - Z M Kovacs-Vajna
- Department of Information Engineering, University of Brescia, Brescia, Italy
| | - K Mullin
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - M A Blumenthal
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - M Mattheisen
- Channing Laboratory, Brigham and Women's Hospital, Boston MA, USA
| | - C Zhang
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - C Lange
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - G Mohapatra
- Molecular Pathology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - L Bertram
- Max-Planck Institute for Molecular Genetics, Neuropsychiatric Genetics Group, Berlin, Germany
| | - R E Tanzi
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
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Chong WWS, Lo IFM, Lam STS, Wang CC, Luk HM, Leung TY, Choy KW. Performance of chromosomal microarray for patients with intellectual disabilities/developmental delay, autism, and multiple congenital anomalies in a Chinese cohort. Mol Cytogenet 2014; 7:34. [PMID: 24926319 PMCID: PMC4055236 DOI: 10.1186/1755-8166-7-34] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 05/06/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Chromosomal microarray (CMA) is currently the first-tier genetic test for patients with idiopathic neuropsychiatric diseases in many countries. Its improved diagnostic yield over karyotyping and other molecular testing facilitates the identification of the underlying causes of neuropsychiatric diseases. In this study, we applied oligonucleotide array comparative genomic hybridization as the molecular genetic test in a Chinese cohort of children with DD/ID, autism or MCA. RESULTS CMA identified 7 clinically significant microduplications and 17 microdeletions in 19.0% (20/105) patients, with size of aberrant regions ranging from 11 kb to 10.7 Mb. Fourteen of the pathogenic copy number variant (CNV) detected corresponded to well known microdeletion or microduplication syndromes. Four overlapped with critical regions of recently identified genomic syndromes. We also identified a rare de novo 2.3 Mb deletion at 8p21.3-21.2 as a pathogenic submicroscopic CNV. We also identified two novel CNVs, one at Xq28 and the other at 12q21.31-q21.33, in two patients (1.9%) with unclear clinical significance. Overall, the detection rate of CMA is comparable to figures previously reported for accurately detect submicroscopic chromosomal imbalances and pathogenic CNVs except mosaicism, balanced translocation and inversion. CONCLUSIONS This study provided further evidence of an increased diagnostic yield of CMA and supported its use as a first line diagnostic tool for Chinese individuals with DD/ID, ASD, and MCA.
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Affiliation(s)
- Wilson Wai Sing Chong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China ; Prenatal genetic diagnosis laboratory, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong SAR, China
| | - Ivan Fai Man Lo
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | | | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China ; Prenatal genetic diagnosis laboratory, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong SAR, China
| | - Ho Ming Luk
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China ; Prenatal genetic diagnosis laboratory, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China ; Prenatal genetic diagnosis laboratory, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, Hong Kong SAR, China ; CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China ; Joint Centre with Utrecht University-Genetic Core, School of Biomedical Science, The Chinese University of Hong Kong, Hong Kong SAR, China
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11
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Xu F, Li L, Schulz VP, Gallagher PG, Xiang B, Zhao H, Li P. Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability. Mol Cytogenet 2014; 7:4. [PMID: 24410907 PMCID: PMC3905969 DOI: 10.1186/1755-8166-7-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/16/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Microarray analysis has been used as the first-tier genetic testing to detect chromosomal imbalances and copy number variants (CNVs) for pediatric patients with intellectual and developmental disabilities (ID/DD). To further investigate the candidate genes and underlying dosage-sensitive mechanisms related to ID, cytogenomic mapping of critical regions and bioinformatic mining of candidate brain-expressed genes (BEGs) and their functional interactions were performed. Critical regions of chromosomal imbalances and pathogenic CNVs were mapped by subtracting known benign CNVs from the Databases of Genomic Variants (DGV) and extracting smallest overlap regions with cases from DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER). BEGs from these critical regions were revealed by functional annotation using Database for Annotation, Visualization, and Integrated Discovery (DAVID) and by tissue expression pattern from Uniprot. Cross-region interrelations and functional networks of the BEGs were analyzed using Gene Relationships Across Implicated Loci (GRAIL) and Ingenuity Pathway Analysis (IPA). RESULTS Of the 1,354 patients analyzed by oligonucleotide array comparative genomic hybridization (aCGH), pathogenic abnormalities were detected in 176 patients including genomic disorders in 66 patients (37.5%), subtelomeric rearrangements in 45 patients (25.6%), interstitial imbalances in 33 patients (18.8%), chromosomal structural rearrangements in 17 patients (9.7%) and aneuploidies in 15 patients (8.5%). Subtractive and extractive mapping defined 82 disjointed critical regions from the detected abnormalities. A total of 461 BEGs was generated from 73 disjointed critical regions. Enrichment of central nervous system specific genes in these regions was noted. The number of BEGs increased with the size of the regions. A list of 108 candidate BEGs with significant cross region interrelation was identified by GRAIL and five significant gene networks involving cell cycle, cell-to-cell signaling, cellular assembly, cell morphology, and gene expression regulations were denoted by IPA. CONCLUSIONS These results characterized ID related cross-region interrelations and multiple networks of candidate BEGs from the detected genomic imbalances. Further experimental study of these BEGs and their interactions will lead to a better understanding of dosage-sensitive mechanisms and modifying effects of human mental development.
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Affiliation(s)
- Fang Xu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Lun Li
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA.,Hubei Bioinformatics and Molecular Imaging Key Laboratory, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Vincent P Schulz
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick G Gallagher
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Bixia Xiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
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Willemsen MH, de Leeuw N, de Brouwer AP, Pfundt R, Hehir-Kwa JY, Yntema HG, Nillesen WM, de Vries BB, van Bokhoven H, Kleefstra T. Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies. Eur J Med Genet 2012; 55:586-98. [DOI: 10.1016/j.ejmg.2012.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 05/05/2012] [Accepted: 05/05/2012] [Indexed: 01/01/2023]
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13
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Honda S, Hayashi S, Nakane T, Imoto I, Kurosawa K, Mizuno S, Okamoto N, Kato M, Yoshihashi H, Kubota T, Nakagawa E, Goto YI, Inazawa J. The incidence of hypoplasia of the corpus callosum in patients with dup (X)(q28) involving MECP2 is associated with the location of distal breakpoints. Am J Med Genet A 2012; 158A:1292-303. [PMID: 22528406 DOI: 10.1002/ajmg.a.35321] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 01/23/2012] [Indexed: 01/09/2023]
Abstract
Duplications of Xq28 harboring the methyl CpG binding protein 2 (MECP2) gene explain approximately 1% of X-linked intellectual disability (XLID). The common clinical features observed in patients with dup(X)(q28) are severe ID, infantile hypotonia, mild dysmorphic features and a history of recurrent infections, and MECP2 duplication syndrome is now recognized as a clinical entity. While some patients with this syndrome have other characteristic phenotypes, the reason for the spectrum of phenotypes has not been clarified. Since dup(X)(q28) rearrangements vary in size and location, genes other than MECP2 might affect the phenotype. We used a high-density oligonucleotide array to carry out precise mapping in eight Japanese families in which dup(X)(q28) was detected using an in-house bacterial artificial chromosome-based microarray to screen cohorts of individuals with multiple congenital anomalies and intellectual disability (MCA/ID) or with XLID. We hypothesized that the size, gene content, and location of dup(X)(q28) may contribute to variable expressively observed in MECP2 duplication syndrome. Genotype-phenotype correlation in our cases together with cases reported in the literature suggested that copy-number gains between two low copy repeats (LCRK1 and LCRL1) are associated with the incidence of hypoplasia of the corpus callosum. Further studies are necessary to understand the mechanism of this association.
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Affiliation(s)
- Shozo Honda
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
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15
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Okamoto N, Hayashi S, Masui A, Kosaki R, Oguri I, Hasegawa T, Imoto I, Makita Y, Hata A, Moriyama K, Inazawa J. Deletion at chromosome 10p11.23-p12.1 defines characteristic phenotypes with marked midface retrusion. J Hum Genet 2012; 57:191-6. [DOI: 10.1038/jhg.2011.154] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Hochstenbach R, Buizer-Voskamp JE, Vorstman JAS, Ophoff RA. Genome arrays for the detection of copy number variations in idiopathic mental retardation, idiopathic generalized epilepsy and neuropsychiatric disorders: lessons for diagnostic workflow and research. Cytogenet Genome Res 2011; 135:174-202. [PMID: 22056632 DOI: 10.1159/000332928] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
We review the contributions and limitations of genome-wide array-based identification of copy number variants (CNVs) in the clinical diagnostic evaluation of patients with mental retardation (MR) and other brain-related disorders. In unselected MR referrals a causative genomic gain or loss is detected in 14-18% of cases. Usually, such CNVs arise de novo, are not found in healthy subjects, and have a major impact on the phenotype by altering the dosage of multiple genes. This high diagnostic yield justifies array-based segmental aneuploidy screening as the initial genetic test in these patients. This also pertains to patients with autism (expected yield about 5-10% in nonsyndromic and 10-20% in syndromic patients) and schizophrenia (at least 5% yield). CNV studies in idiopathic generalized epilepsy, attention-deficit hyperactivity disorder, major depressive disorder and Tourette syndrome indicate that patients have, on average, a larger CNV burden as compared to controls. Collectively, the CNV studies suggest that a wide spectrum of disease-susceptibility variants exists, most of which are rare (<0.1%) and of variable and usually small effect. Notwithstanding, a rare CNV can have a major impact on the phenotype. Exome sequencing in MR and autism patients revealed de novo mutations in protein coding genes in 60 and 20% of cases, respectively. Therefore, it is likely that arrays will be supplanted by next-generation sequencing methods as the initial and perhaps ultimate diagnostic tool in patients with brain-related disorders, revealing both CNVs and mutations in a single test.
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Affiliation(s)
- R Hochstenbach
- Division of Biomedical Genetics, Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands.
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Going BAC or oligo microarray to the well: a commentary on Clinical application of array-based comparative genomic hybridization by two-stage screening for 536 patients with mental retardation and multiple congenital anomalies. J Hum Genet 2011; 56:104-5. [PMID: 21228794 DOI: 10.1038/jhg.2010.168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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