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Kim U, Jung YM, Oh S, Bae JH, Lee J, Park CW, Park JS, Jun JK, Lee SM. Chromosomal Microarray Analysis in Fetuses With Ultrasonographic Soft Markers: A Meta-Analysis of the Current Evidence. J Korean Med Sci 2024; 39:e70. [PMID: 38442716 PMCID: PMC10911939 DOI: 10.3346/jkms.2024.39.e70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/17/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Ultrasonographic soft markers are normal variants, rather than fetal abnormalities, and guidelines recommend a detailed survey of fetal anatomy to determine the necessity of antenatal karyotyping. Anecdotal reports have described cases with ultrasonographic soft markers in which chromosomal microarray analysis (CMA) revealed pathogenic copy number variants (CNVs) despite normal results on conventional karyotyping, but CMA for ultrasonographic soft markers remains a matter of debate. In this systematic review, we evaluated the clinical significance of CMA for pregnancies with isolated ultrasonographic soft markers and a normal fetal karyotype. METHODS An electronic search was conducted by an experienced librarian through the MEDLINE, Embase, and Cochrane CENTRAL databases. We reviewed 3,338 articles (3,325 identified by database searching and 13 by a hand search) about isolated ultrasonographic soft markers, and seven ultrasonographic markers (choroid plexus cysts, echogenic bowel, echogenic intracardiac focus, hypoplastic nasal bone, short femur [SF], single umbilical artery, and urinary tract dilatation) were included for this study. RESULTS Seven eligible articles were included in the final review. Pathogenic or likely pathogenic CNVs were found in fetuses with isolated ultrasonographic soft markers and a normal karyotype. The overall prevalence of pathogenic or likely pathogenic CNVs was 2.0% (41 of 2,048). The diagnostic yield of CMA was highest in fetuses with isolated SF (9 of 225, 3.9%). CONCLUSION CMA could aid in risk assessment and pregnancy counseling in pregnancies where the fetus has isolated ultrasonographic soft markers along with a normal karyotype.
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Affiliation(s)
- Uisuk Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Young Mi Jung
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Sohee Oh
- Department of Biostatistics, Seoul Metropolitan Government-Seoul National University Hospital Boramae Medical Center, Seoul, Korea
| | - Ji Hye Bae
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Jeesun Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Chan-Wook Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Joong Shin Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Kwan Jun
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Seung Mi Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea.
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Antony I, Narasimhan M, Shen R, Prakasam R, Kaushik K, Chapman G, Kroll KL. Duplication Versus Deletion Through the Lens of 15q13.3: Clinical and Research Implications of Studying Copy Number Variants Associated with Neuropsychiatric Disorders in Induced Pluripotent Stem Cell-Derived Neurons. Stem Cell Rev Rep 2023; 19:639-650. [PMID: 36370261 PMCID: PMC10115185 DOI: 10.1007/s12015-022-10475-0] [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] [Accepted: 10/25/2022] [Indexed: 11/15/2022]
Abstract
Copy number variants (CNVs), involving duplication or deletion of susceptible intervals of the human genome, underlie a range of neurodevelopmental and neuropsychiatric disorders. As accessible in vivo animal models of these disorders often cannot be generated, induced pluripotent stem cell (iPSC) models derived from patients carrying these CNVs can reveal alterations of brain development and neuronal function that contribute to these disorders. CNVs involving deletion versus duplication of a particular genomic interval often result both in distinct clinical phenotypes and in differential phenotypic penetrance. This review initially focuses on CNVs at 15q13.3, which contribute to autism spectrum disorder, attention deficit/hyperactivity disorder, and schizophrenia. Like most CNVs, deletions at 15q13.3 usually cause severe clinical phenotypes, while duplications instead result in highly variable penetrance, with some carriers exhibiting no clinical phenotype. Here, we describe cellular and molecular phenotypes seen in iPSC-derived neuronal models of 15q13.3 duplication and deletion, which may contribute both to the differential clinical consequences and phenotypic penetrance. We then relate this work to many other CNVs involving both duplication and deletion, summarizing findings from iPSC studies and their relationship to clinical phenotype. Together, this work highlights how CNVs involving duplication versus deletion can differentially alter neural development and function to contribute to neuropsychiatric disorders. iPSC-derived neuronal models of these disorders can be used both to understand the underlying neurodevelopmental alterations and to develop pharmacological or molecular approaches for phenotypic rescue that may suggest leads for patient intervention. Top: Deletion versus duplication of the same genomic interval results in different clinical phenotypes and degrees of phenotypic penetrance. Example findings schematized. Bottom: iPSC-derived neurons from individuals with these CNVs involving deletion versus duplication likewise often differential phenotypes (increases or decreases) in the categories shown. Figure created with BioRender.com.
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Affiliation(s)
- Irene Antony
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Mishka Narasimhan
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Renata Shen
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Ramachandran Prakasam
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Komal Kaushik
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Gareth Chapman
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
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3
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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Li Z, Li Y, Li N, Shen L, Liu A. Silencing GOLGA8B inhibits cell invasion and metastasis by suppressing STAT3 signaling pathway in lung squamous cell carcinoma. Clin Sci (Lond) 2022; 136:895-909. [PMID: 35593117 DOI: 10.1042/cs20220128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/06/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
Abstract
Changes to some Golgi subfamily member proteins are reported to be involved in tumor metastasis. However, the functional role and potential mechanism of the Golgi A8 family member B (GOLGA8B) in lung squamous cell carcinoma (LUSC) remains unknown. In the present study, GOLGA8B expression was detected using qRT-PCR, Western blot, and immunohistochemistry (IHC). In vivo animal experiments and in vitro functional assays were performed to explore the function of GOLGA8B in LUSC. Luciferase assays were performed to investigate the underlying targets of GOLGA8B in LUSC. GOLGA8B was shown to be highly expressed in LUSC metastasis tissue, and significantly associated with the distant metastasis-free survival of LUSC patients. Loss-of-function assays indicated that silencing GOLGA8B suppressed LUSC cell tumorigenesis in vivo and weakened in vitro invasion and migration. GOLGA8B silencing-induced inhibition of invasion and migration was associated with the inactivation of STAT3 signaling. Importantly, these results showed that the number of circulating tumor cells (CTCs) was markedly higher in the GOLGA8B silencing group than in the control vector group. GOLGA8B expression was positively associated with p-STAT3 expression in LUSC tissue. Study findings revealed a novel mechanism by which GOLGA8B promotes tumor metastasis in LUSC cells and suggests that this protein could be a promising target for antitumor metastasis therapy in LUSC patients.
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Affiliation(s)
- Zhanzhan Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, China
| | - Yanyan Li
- Department of Nursing, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, China
| | - Na Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, China
| | - Liangfang Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, China
| | - Aibin Liu
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
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Iosifidis C, Liu J, Gale T, Ellingford JM, Campbell C, Ingram S, Chandler K, Parry NRA, Black GC, Sergouniotis PI. Clinical and genetic findings in TRPM1-related congenital stationary night blindness. Acta Ophthalmol 2022; 100:e1332-e1339. [PMID: 35633130 DOI: 10.1111/aos.15186] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/05/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE Congenital stationary night blindness (CSNB) is a heterogeneous group of Mendelian retinal disorders that present in childhood. Biallelic variants altering the protein-coding region of the TRPM1 gene are one of the commonest causes of CSNB. Here, we report the clinical and genetic findings in 10 unrelated individuals with TRPM1-retinopathy. METHODS Study subjects were recruited through a tertiary clinical ophthalmic genetic service at Manchester, UK. All participants underwent visual electrodiagnostic testing and panel-based genetic analysis. RESULTS Study subjects had a median age of 8 years (range: 3-20 years). All probands were myopic and had electroretinographic findings in keeping with complete CSNB. Notably, three probands reported no night vision problems. Fourteen different disease-associated TRPM1 variants were detected. One individual was homozygous for the NM_001252024.2 (TRPM1):c.965 + 29G>A variant and a mini-gene assay highlighted that this change results in mis-splicing and premature protein termination. Additionally, two unrelated probands who had CSNB and mild neurodevelopmental abnormalities were found to carry a 15q13.3 microdeletion. This copy number variant encompasses seven genes, including TRPM1, and was encountered in the heterozygous state and in trans with a missense TRPM1 variant in each case. CONCLUSION Our findings highlight the importance of comprehensive genomic analysis, beyond the exons and protein-coding regions of genes, for individuals with CSNB. When this characteristic retinal phenotype is accompanied by extraocular findings (including learning and/or behavioural difficulties), a 15q13.3 microdeletion should be suspected. Focused analysis (e.g. microarray testing) is recommended to look for large-scale deletions encompassing TRPM1 in patients with CSNB and neurodevelopmental abnormalities.
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Affiliation(s)
- Christos Iosifidis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
- Manchester Royal Eye Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Jingshu Liu
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
| | - Theodora Gale
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Jamie M. Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Stuart Ingram
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Kate Chandler
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Neil R. A. Parry
- Manchester Royal Eye Hospital Manchester University NHS Foundation Trust Manchester UK
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
| | - Graeme C. Black
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Panagiotis I. Sergouniotis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
- Manchester Royal Eye Hospital Manchester University NHS Foundation Trust Manchester UK
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine University of Ljubljana Ljubljana Slovenia
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Cheng MC, Chien WH, Huang YS, Fang TH, Chen CH. Translational Study of Copy Number Variations in Schizophrenia. Int J Mol Sci 2021; 23:ijms23010457. [PMID: 35008879 PMCID: PMC8745588 DOI: 10.3390/ijms23010457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/11/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Rare copy number variations (CNVs) are part of the genetics of schizophrenia; they are highly heterogeneous and personalized. The CNV Analysis Group of the Psychiatric Genomic Consortium (PGC) conducted a large-scale analysis and discovered that recurrent CNVs at eight genetic loci were pathogenic to schizophrenia, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.23, 15q13.3, distal 16p11.2, proximal 16p11.2, and 22q11.2. We adopted a two-stage strategy to translate this knowledge into clinical psychiatric practice. As a screening test, we first developed a real-time quantitative PCR (RT-qPCR) panel that simultaneously detected these pathogenic CNVs. Then, we tested the utility of this screening panel by investigating a sample of 557 patients with schizophrenia. Chromosomal microarray analysis (CMA) was used to confirm positive cases from the screening test. We detected and confirmed thirteen patients who carried CNVs at these hot loci, including two patients at 1q21.1, one patient at 7q11.2, three patients at 15q13.3, two patients at 16p11.2, and five patients at 22q11.2. The detection rate in this sample was 2.3%, and the concordance rate between the RT-qPCR test panel and CMA was 100%. Our results suggest that a two-stage approach is cost-effective and reliable in achieving etiological diagnosis for some patients with schizophrenia and improving the understanding of schizophrenia genetics.
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Affiliation(s)
- Min-Chih Cheng
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 981, Taiwan;
| | - Wei-Hsien Chien
- Department of Occupational Therapy, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan;
| | - Yu-Shu Huang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Ting-Hsuan Fang
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- Department and Institute of Biomedical Sciences, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence:
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7
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Muthusamy K, El-Jabali A, Ongie LJ, Dhamija R, Babovic-Vuksanovic D. Neurofibromatosis 1 in the setting of dual diagnosis: Diagnostic and management conundrums. Am J Med Genet A 2021; 188:911-918. [PMID: 34797032 DOI: 10.1002/ajmg.a.62575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/27/2021] [Accepted: 10/29/2021] [Indexed: 11/07/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a common neurocutaneous disorder characterized by development of pigmentary skin changes, neurogenic tumors, and other manifestations involving multiple organ systems. Penetrance is complete, though expressivity is quite variable even among the family members. Given that NF1 is a common hereditary condition, existence of a second genetic disorder in NF1 patients is not unexpected. During comprehensive evaluations of individuals with NF1, we encountered 11 patients with dual diagnosis who contributed to phenotypic complexity and challenges for long-term management. Examples include Prader-Willi Syndrome, Autosomal Dominant Polycystic Kidney Disease, Down syndrome, infantile myofibromatosis, Craniosynostosis, cleft lip and palate, 47,XYY, 22q11.2 duplication, 15q13.3 deletion syndrome, and BRCA2- and ATM- related cancer predisposition syndromes. Presence of dysmorphism, developmental delay, atypical tumors, and family history of other genetic disorders including cancers appears as determinants to consider a second genetic etiology and helps to differentiate from an extreme phenotypic spectrum of NF1. Clinicians should have high index of suspicion to exclude coexisting disorders, as apart from providing comprehensive medical care. This also has potential implications in genetic counseling. Long-term effects of the synergistic mechanisms leading to phenotypic complexity and patient outcomes are yet to be characterized, with follow-up needed.
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Affiliation(s)
- Karthik Muthusamy
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Laura J Ongie
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Phoenix, Arizona, USA.,Department of Neurology, Mayo Clinic, Phoenix, Arizona, USA
| | - Dusica Babovic-Vuksanovic
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Whitney R, Nair A, McCready E, Keller AE, Adil IS, Aziz AS, Borys O, Siu K, Shah C, Meaney BF, Jones K, RamachandranNair R. The spectrum of epilepsy in children with 15q13.3 microdeletion syndrome. Seizure 2021; 92:221-229. [PMID: 34601452 DOI: 10.1016/j.seizure.2021.09.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/02/2021] [Accepted: 09/23/2021] [Indexed: 12/31/2022] Open
Abstract
PURPOSE To further define the epilepsy phenotype in a cohort of children with 15q13.3 microdeletion syndrome. METHODS We retrospectively reviewed the phenotypic spectrum of all children aged < 18 years with epilepsy and 15q13.3 microdeletion syndrome. RESULTS Thirteen children were included, 69% were female. The median age of children in the cohort was 12 years (age range: 3 years-15 years). Median age at seizure onset was 4 years. Eleven children (85%) had intellectual disability. Nine of 13 children (69%) had a history of typical absence seizures with median age of onset at 5 years (2 had absence status epilepticus). Thirty-one percent (4/13) had focal with impaired awareness non-motor onset seizures. ILAE recognized absence epilepsy syndromes were diagnosed in 6/13 (46%). The remainder were classified as having genetic generalized epilepsies with overlap clinical features, combined or focal epilepsies. Electroencephalogram in the cohort showed generalized (85%) and focal epileptiform discharges (62%) and posterior dominant rhythm slowing (33%). One child had electrical status epilepticus of sleep. Neuroimaging was performed in 5 children (38%) and revealed abnormal findings in 3. Seizures were drug resistant in a third of the cohort. Valproate resulted in seizure freedom in 5 (42%). Oxcarbazepine caused clinical worsening in one child with combined seizure types. Two children tried cannabidiol and one tried the ketogenic diet; neither was effective. CONCLUSIONS The epilepsy phenotype in children with 15q13.3 microdeletion syndrome is defined by childhood onset absence seizures, and may have atypical features such as, early onset absences, persistence into adolescence, status epilepticus, intellectual disability and treatment resistance. Focal seizures and focal EEG findings may be observed and should be treated cautiously, given the possibility of combined seizure types. Valproate appeared effective, although other treatments must be explored further.
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Affiliation(s)
- Robyn Whitney
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON, Canada.
| | - Arjun Nair
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON, Canada
| | - Elizabeth McCready
- Division of Clinical Pathology, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Anne E Keller
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON, Canada
| | - Ishita Siddiq Adil
- Pediatric Neurology Clinic, Oakville, ON, Canada; Division of Neurology, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Aly Shah Aziz
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON, Canada; Pediatric Neurology Clinic, Oakville, ON, Canada
| | - Oksana Borys
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON, Canada; Pediatric Neurology Clinic, Oakville, ON, Canada
| | - Kaitlyn Siu
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON, Canada
| | - Chintan Shah
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON, Canada
| | - Brandon F Meaney
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON, Canada
| | - Kevin Jones
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON, Canada
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Huang H, Cai M, Ma W, Lin N, Xu L. Chromosomal Microarray Analysis for the Prenatal Diagnosis in Fetuses with Nasal Bone Hypoplasia: A Retrospective Cohort Study. Risk Manag Healthc Policy 2021; 14:1533-1540. [PMID: 33889037 PMCID: PMC8054820 DOI: 10.2147/rmhp.s286038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
Background Previous studies have shown a strong correlation between fetal nasal bone hypoplasia and chromosomal anomaly; however, there is little knowledge on the associations of fetal nasal bone hypoplasia with chromosomal microdeletions and microduplications until now. Chromosomal microarray analysis (CMA) is a high-resolution molecular genetic tool that is effective to detect submicroscopic anomalies including chromosomal microdeletions and microduplications that cannot be detected by karyotyping. This study aimed to examine the performance of CMA for the prenatal diagnosis of nasal bone hypoplasia in the second and third trimesters. Subjects and Methods A total of 84 pregnant women in the second and third trimesters with fetal nasal bone hypoplasia, as revealed by ultrasound examinations, were enrolled, and all women underwent karyotyping and CMA with the Affymetrix CytoScan 750K GeneChip Platform. The subjects included 32 cases with fetal nasal bone hypoplasia alone and 52 cases with fetal nasal bone hypoplasia combined with other ultrasound abnormalities, and the prevalence of genomic abnormality was compared between these two groups. Results Karyotyping detected 21 cases of chromosomal anomaly in the 84 study subjects (21/84, 25%), including trisomy 21 (14 cases), trisomy 18 (3 cases), 46, del (4)(p16) karyotype (2 cases), 47, XYY syndrome (1 case) and 46, XY, del (5) (p15) karyotype (1 case). CMA detected additional four fetuses with pathogenic copy number variations (CNVs) and six fetuses with uncertain clinical significance (VOUS). No significant difference was detected in the prevalence of genomic abnormality in fetuses with nasal bone hypoplasia alone and in combination with other ultrasound abnormalities (13/32 vs 18/52; χ2 = 0.31, P > 0.05). The pregnancy was terminated in 21 fetuses detected with chromosomal abnormality and 4 fetuses detected with pathogenic CNVs. Among the other six fetuses detected with VOUS, the parents chose to continue the pregnancy, and the newborns all had normal clinical phenotypes. Conclusion In addition to chromosomal abnormalities identified in 21 fetuses by karyotyping, CMA detected additional 10 fetuses with abnormal CNVs (10/84, 11.9%) in the study population. CMA is a promising powerful tool for prenatal diagnosis that may provide valuable data for the accurate assessment of fetal prognosis and the decision of pregnancy continuation during the prenatal clinical counseling.
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Affiliation(s)
- Hailong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Meiying Cai
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Wei Ma
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China.,School of Clinical Medicine, Fujian Medical University, Fuzhou City, Fujian Province, 350122, People's Republic of China
| | - Na Lin
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
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10
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Delle Fave M, Cordonnier M, Vallee L, Condroyer C, Zeitz C, Balikova I. Congenital stationary night blindness in a patient with mild learning disability due to a compound heterozygous microdeletion of 15q13 and a missense mutation in TRPM1. Ophthalmic Genet 2021; 42:296-299. [PMID: 33691579 DOI: 10.1080/13816810.2021.1897846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The complete form of congenital stationary night blindness (cCSNB) represents a non-progressive retinal disorder characterized by night vision problems and often congenital nystagmus, reduced vision, high myopia, strabismus and normal fundus appearance. Clinically this form of CSNB can be diagnosed by full-field electroretinogram. The mode of inheritance can be X-linked and autosomal recessive with mutations in genes coding for proteins mainly present at the dendritic tips of ON-bipolar cells. Mutations in NYX, GRM6, GPR179, LRIT3 and TRPM1 lead to this condition. The latter gene defect represents the major form underlying cCSNBC. It codes for the melastatin-related transient receptor 1 expressed in the inner nuclear layer of the retina, with the protein localized in ON-bipolar cells. To date, various homozygous or compound heterozygous mutations in TRPM1 have been reported. Small chromosomal rearrangements are frequent cause of mental retardation. In rare cases deletions can overlap with a mutation on the remaining chromosome and lead to a recessive disorder. Here, we describe a patient with mild neurological deficiencies and cCSNB caused by a microdeletion on 15q32 overlapping with a TRPM1 variant.
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Affiliation(s)
- M Delle Fave
- Ophthalmology Service, CUB Hopital Erasme, Brussels, Belgium
| | - M Cordonnier
- Ophthalmology Service, CUB Hopital Erasme, Brussels, Belgium
| | - L Vallee
- Neuropediatric Service, University Hospital Lille, Lille, France
| | - C Condroyer
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - C Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - I Balikova
- Ophthalmology Service, University Hospital Gasthuisberg, Leuven, Belgium
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11
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Pavone P, Pappalardo XG, Ohazuruike UNN, Striano P, Parisi P, Corsello G, Marino SD, Ruggieri M, Parano E, Falsaperla R. Chromosome 15q BP4-BP5 Deletion in a Girl with Nocturnal Frontal Lobe Epilepsy, Migraine, Circumscribed Hypertrichosis, and Language Impairment. J Epilepsy Res 2020; 10:84-91. [PMID: 33659201 PMCID: PMC7903043 DOI: 10.14581/jer.20014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/06/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023] Open
Abstract
The 15q13.3 microdeletion (microdel15q13.3) syndrome (OMIM 612001) has been reported in healthy subjects as well as in individuals with a wide spectrum of clinical manifestations ranging from mild to severe neurological disorders, including developmental delay/intellectual disability, autism spectrum disorder, schizophrenia, epilepsy, behavioral problems and speech dysfunction. This study explored the link between this genomic rearrangement and nocturnal frontal lobe epilepsy (NFLE), which could improve the clinical interpretation. A clinical and genomic investigation was carried out on an 8-year-girl with a de novo deletion flanking the breakpoints (BPs) 4 and 5 of 15q13.3 detected by array comparative genomic hybridization analysis, affected by NFLE, migraine with aura, minor facial features, mild cognitive and language impairment, and circumscribed hypertrichosis. Literature survey of clinical studies was included. Nine years follow-up have displayed a benign course of the epileptic disorder with a progressive reduction and disappearance of the epileptic seizures, mild improvement of cognitive and language skills, partial cutaneous hypertrichosis regression, but stable ongoing of migraine episodes. A likely relationship between the BP4–BP5 deletion and NFLE with other symptoms presented by the girl is discussed together with a review of the literature on phenotypic features in microdel15q13.3.
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Affiliation(s)
- Piero Pavone
- Unit of Pediatrics and Pediatric Emergency, University Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
| | - Xena Giada Pappalardo
- Unit of Catania, Institute for Biomedical Research and Innovation (IRIB), National Council of Research, Catania, Italy.,Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
| | | | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS 'G. Gaslini' Institute, Genoa, Italy
| | - Pasquale Parisi
- Child Neurology, NESMOS Department, Faculty of Medicine & Psychology, "Sapienza" University, c/o Sant'Andrea Hospital, Rome, Italy
| | - Giovanni Corsello
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | | | - Martino Ruggieri
- Unit of Pediatrics and Pediatric Emergency, University Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
| | - Enrico Parano
- Unit of Catania, Institute for Biomedical Research and Innovation (IRIB), National Council of Research, Catania, Italy
| | - Raffaele Falsaperla
- Unit of Neonatology University Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
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12
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Bekpen C, Tautz D. Human core duplicon gene families: game changers or game players? Brief Funct Genomics 2020; 18:402-411. [PMID: 31529038 PMCID: PMC6920530 DOI: 10.1093/bfgp/elz016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/01/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023] Open
Abstract
Illuminating the role of specific gene duplications within the human lineage can provide insights into human-specific adaptations. The so-called human core duplicon gene families have received particular attention in this respect, due to special features, such as expansion along single chromosomes, newly acquired protein domains and signatures of positive selection. Here, we summarize the data available for 10 such families and include some new analyses. A picture emerges that suggests broad functions for these protein families, possibly through modification of core cellular pathways. Still, more dedicated studies are required to elucidate the function of core-duplicons gene families and how they have shaped adaptations and evolution of humans.
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Affiliation(s)
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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13
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Paduano F, Colao E, Loddo S, Orlando V, Trapasso F, Novelli A, Perrotti N, Iuliano R. 7q35 Microdeletion and 15q13.3 and Xp22.33 Microduplications in a Patient with Severe Myoclonic Epilepsy, Microcephaly, Dysmorphisms, Severe Psychomotor Delay and Intellectual Disability. Genes (Basel) 2020; 11:genes11050525. [PMID: 32397165 PMCID: PMC7288449 DOI: 10.3390/genes11050525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 11/16/2022] Open
Abstract
Copy number variations (CNVs) play a key role in the pathogenesis of several diseases, including a wide range of neurodevelopmental disorders. Here, we describe the detection of three CNVs simultaneously in a female patient with evidence of severe myoclonic epilepsy, microcephaly, hypertelorism, dimorphisms as well as severe psychomotor delay and intellectual disability. Array-CGH analysis revealed a ~240 kb microdeletion at the 7q35 inherited from her father, a ∼538 kb microduplication at the 15q13.3 region and a ∼178 kb microduplication at Xp22.33 region, both transmitted from her mother. The microdeletion in 7q35 was included within an intragenic region of the contactin associated protein-like 2 (CNTNAP2) gene, whereas the microduplications at 15q13.3 and Xp22.33 involved the cholinergic receptor nicotinic α 7 subunit (CHRNA7) and the cytokine receptor-like factor 2 (CRLF2) genes, respectively. Here, we describe a female patient harbouring three CNVs whose additive contribution could be responsible for her clinical phenotypes.
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MESH Headings
- Adult
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 15/ultrastructure
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 7/ultrastructure
- Chromosomes, Human, X/genetics
- Chromosomes, Human, X/ultrastructure
- Consanguinity
- DNA Copy Number Variations
- Epilepsies, Myoclonic/genetics
- Female
- Gene Duplication
- Genetic Association Studies
- Humans
- Membrane Proteins/genetics
- Microcephaly/genetics
- Nerve Tissue Proteins/genetics
- Neurodevelopmental Disorders/genetics
- Pedigree
- Receptors, Cytokine/genetics
- Sequence Deletion
- Tissue Array Analysis
- alpha7 Nicotinic Acetylcholine Receptor/genetics
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Affiliation(s)
- Francesco Paduano
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
- Tecnologica Research Institute and Marrelli Health, Biomedical Section, Stem Cells Unit, 88900 Crotone, Italy
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus S. Venuta, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Emma Colao
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
| | - Sara Loddo
- Medical Genetics Laboratory, Bambino Gesù Pediatric Hospital, IRCCS, 00165 Rome, Italy; (S.L.); (V.O.); (A.N.)
| | - Valeria Orlando
- Medical Genetics Laboratory, Bambino Gesù Pediatric Hospital, IRCCS, 00165 Rome, Italy; (S.L.); (V.O.); (A.N.)
| | - Francesco Trapasso
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, Campus S. Venuta, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Antonio Novelli
- Medical Genetics Laboratory, Bambino Gesù Pediatric Hospital, IRCCS, 00165 Rome, Italy; (S.L.); (V.O.); (A.N.)
| | - Nicola Perrotti
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
- Department of Health Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy
| | - Rodolfo Iuliano
- Medical Genetics Unit, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.P.); (E.C.); (F.T.); (N.P.)
- Department of Health Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy
- Correspondence:
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14
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Jagannath V, Grünblatt E, Theodoridou A, Oneda B, Roth A, Gerstenberg M, Franscini M, Traber-Walker N, Correll CU, Heekeren K, Rössler W, Rauch A, Walitza S. Rare copy number variants in individuals at clinical high risk for psychosis: Enrichment of synaptic/brain-related functional pathways. Am J Med Genet B Neuropsychiatr Genet 2020; 183:140-151. [PMID: 31742845 DOI: 10.1002/ajmg.b.32770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/08/2019] [Accepted: 10/23/2019] [Indexed: 11/07/2022]
Abstract
Schizophrenia is a complex and chronic neuropsychiatric disorder, with a heritability of around 60-80%. Large (>100 kb) rare (<1%) copy number variants (CNVs) occur more frequently in schizophrenia patients compared to controls. Currently, there are no studies reporting genome-wide CNVs in clinical high risk for psychosis (CHR-P) individuals. The aim of this study was to investigate the role of rare genome-wide CNVs in 84 CHR-P individuals and 124 presumably healthy controls. There were no significant differences in all rare CNV frequencies and sizes between CHR-P individuals and controls. However, brain-related CNVs and brain-related deletions were significantly more frequent in CHR-P individuals than controls. In CHR-P individuals, significant associations were found between brain-related CNV carriers and attenuated positive symptoms syndrome or cognitive disturbances (OR = 3.07, p = .0286). Brain-related CNV carriers experienced significantly higher negative symptoms (p = .0047), higher depressive symptoms (p = .0175), and higher disturbances of self and surroundings (p = .0029) than noncarriers. Furthermore, enrichment analysis of genes was performed in the regions of rare CNVs using three independent methods, which confirmed significant clustering of predefined genes involved in synaptic/brain-related functional pathways in CHR-P individuals. These results suggest that rare CNVs might affect synaptic/brain-related functional pathways in CHR-P individuals.
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Affiliation(s)
- Vinita Jagannath
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Anastasia Theodoridou
- The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Alexander Roth
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Miriam Gerstenberg
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Maurizia Franscini
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Nina Traber-Walker
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Christoph U Correll
- Department of Psychiatry, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, New York.,Department of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York.,The Feinstein Institute for Medical Research, Manhasset, New York.,Department of Child and Adolescent Psychiatry, Charité Universitätsmedizin, Berlin, Germany
| | - Karsten Heekeren
- The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland
| | - Wulf Rössler
- The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Anita Rauch
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland
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15
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Pavone P, Ruggieri M, Marino SD, Corsello G, Pappalardo X, Polizzi A, Parano E, Romano C, Marino S, Praticò AD, Falsaperla R. Chromosome 15q BP3 to BP5 deletion is a likely locus for speech delay and language impairment: Report on a four-member family and an unrelated boy. Mol Genet Genomic Med 2020; 8:e1109. [PMID: 31991071 PMCID: PMC7196468 DOI: 10.1002/mgg3.1109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 01/13/2023] Open
Abstract
Background Deletions in chromosome 15q13 have been reported both in healthy people and individuals with a wide range of behavioral and neuropsychiatric disturbances. Six main breakpoint (BP) subregions (BP1‐BP6) are mapped to the 15q13 region and three further embedded BP regions (BP3‐BP5). The deletion at BP4‐BP5 is the rearrangement most frequently observed compared to other known deletions in BP3‐BP5 and BP3‐BP4 regions. Deletions of each of these three regions have previously been implicated in a variable range of clinical phenotypes, including minor dysmorphism, developmental delay/intellectual disability, epilepsy, autism spectrum disorders, behavioral disturbances, and speech disorders. Of note, no overt clinical difference among each group of BP region deletions has been recorded so far. Methods We report on a four‐member family plus an additional unrelated boy affected by a BP3‐BP5 deletion that presented with typical clinical signs including speech delay and language impairment. A review of the clinical features associated with the three main groups of BP regions (BP4‐BP5, BP3‐BP5, and BP3‐BP4) deletions is reported. Results Array‐CGH analysis revealed in the mother (case 1) and in her three children (cases 2, 3, and 4), as well as in the unrelated boy (case 5), the following rearrangement: arr (hg19) 15q13.1‐q13.3 (29.213.402–32.510.863) x1. Conclusion This report, along with other recent observations, suggests the hypothesis that the BP region comprised between BP3 and BP5 in chromosome 15q13 is involved in several brain human dysfunctions, including impairment of the language development and, its deletion, may be directly or indirectly responsible for the speech delay and language deficit in the affected individuals.
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Affiliation(s)
- Piero Pavone
- Unit of Clinical Pediatrics, University Hospital "Policlinico-Vittorio Emanuele", University of Catania, Catania, Italy.,Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Simona D Marino
- Units of Pediatrics and Pediatric Emergency, University Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
| | - Giovanni Corsello
- Units of Pediatrics and Neonatal Intensive Care, Department of Health Promotion of Maternal-Infantile Care and of Excellence Internal and Specialist Medicine "G. D'Alessandro" [PROMISE], University of Palermo, Palermo, Italy
| | - Xena Pappalardo
- National Council of Research, Institute for Research and Biomedical Innovation (IRIB), Unit of Catania, Catania, Italy
| | - Agata Polizzi
- Chair of Pediatrics, Department of Educational Sciences, University of Catania, Catania, Italy
| | - Enrico Parano
- National Council of Research, Institute for Research and Biomedical Innovation (IRIB), Unit of Catania, Catania, Italy
| | - Catia Romano
- Units of Pediatrics and Pediatric Emergency, University Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
| | - Silvia Marino
- Units of Pediatrics and Pediatric Emergency, University Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
| | - Andrea Domenico Praticò
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Raffaele Falsaperla
- Units of Pediatrics and Pediatric Emergency, University Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
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16
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Glessner JT, Li J, Wang D, March M, Lima L, Desai A, Hadley D, Kao C, Gur RE, Cohen N, Sleiman PMA, Li Q, Hakonarson H. Copy number variation meta-analysis reveals a novel duplication at 9p24 associated with multiple neurodevelopmental disorders. Genome Med 2017; 9:106. [PMID: 29191242 PMCID: PMC5709845 DOI: 10.1186/s13073-017-0494-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/14/2017] [Indexed: 12/24/2022] Open
Abstract
Background Neurodevelopmental and neuropsychiatric disorders represent a wide spectrum of heterogeneous yet inter-related disease conditions. The overlapping clinical presentations of these diseases suggest a shared genetic etiology. We aim to identify shared structural variants spanning the spectrum of five neuropsychiatric disorders. Methods We investigated copy number variations (CNVs) in five cohorts, including schizophrenia (SCZ), bipolar disease (BD), autism spectrum disorders (ASD), attention deficit hyperactivity disorder (ADHD), and depression, from 7849 cases and 10,799 controls. CNVs were called based on intensity data from genome-wide SNP arrays and CNV frequency was compared between cases and controls in each disease cohort separately. Meta-analysis was performed via a gene-based approach. Quantitative PCR (qPCR) was employed to validate novel significant loci. Results In our meta-analysis, two genes containing CNVs with exonic overlap reached genome-wide significance threshold of meta P value < 9.4 × 10−6 for deletions and 7.5 × 10−6 for duplications. We observed significant overlap between risk CNV loci across cohorts. In addition, we identified novel significant associations of DOCK8/KANK1 duplications (meta P value = 7.5 × 10−7) across all cohorts, and further validated the CNV region with qPCR. Conclusions In the first large scale meta-analysis of CNVs across multiple neurodevelopmental/psychiatric diseases, we uncovered novel significant associations of structural variants in the locus of DOCK8/KANK1 shared by five diseases, suggesting common etiology of these clinically distinct neurodevelopmental conditions. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0494-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph T Glessner
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jin Li
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Dai Wang
- Janssen Research & Development, LLC, Raritan, NJ, 08869, USA
| | - Michael March
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Leandro Lima
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Akshatha Desai
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Dexter Hadley
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Charlly Kao
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nadine Cohen
- Janssen Research & Development, LLC, Raritan, NJ, 08869, USA
| | - Patrick M A Sleiman
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qingqin Li
- Janssen Research & Development, LLC, Titusville, NJ, 08560, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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