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Khowal S, Zhang D, Yong WH, Heaney AP. Whole-exome sequencing reveals genetic variants that may play a role in neurocytomas. J Neurooncol 2024; 166:471-483. [PMID: 38319496 DOI: 10.1007/s11060-024-04567-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024]
Abstract
OBJECTIVES Neurocytomas (NCs) are rare intracranial tumors that can often be surgically resected. However, disease course is unpredictable in many patients and medical therapies are lacking. We have used whole exome sequencing to explore the molecular etiology for neurocytoma and assist in target identification to develop novel therapeutic interventions. METHODS We used whole exome sequencing (WES) to compare the molecular landscape of 21 primary & recurrent NCs to five normal cerebellar control samples. WES data was analyzed using the Qiagen Clinical Insight program, variants of interest (VOI) were interrogated using ConSurf, ScoreCons, & Ingenuity Pathway Analysis Software to predict their potential functional effects, and Copy number variations (CNVs) in the genes of interest were analyzed by Genewiz (Azenta Life Sciences). RESULTS Of 40 VOI involving thirty-six genes, 7 were pathogenic, 17 likely-pathogenic, and 16 of uncertain-significance. Of seven pathogenic NC associated variants, Glucosylceramidase beta 1 [GBA1 c.703T > C (p.S235P)] was mutated in 5/21 (24%), Coagulation factor VIII [F8 c.3637dupA (p.I1213fs*28)] in 4/21 (19%), Phenylalanine hydroxylase [PAH c.975C > A (p.Y325*)] in 3/21 (14%), and Fanconi anemia complementation group C [FANCC c.1162G > T (p.G388*)], Chromodomain helicase DNA binding protein 7 [CHD7 c.2839C > T (p.R947*)], Myosin VIIA [MYO7A c.940G > T (p.E314*)] and Dynein axonemal heavy chain 11 [DNAH11 c.3544C > T (p.R1182*)] in 2/21 (9.5%) NCs respectively. CNVs were noted in 85% of these latter 7 genes. Interestingly, a Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2 [CTDSP2 c.472G > A (p.E158K)] of uncertain significance was also found in > 70% of NC cases. INTERPRETATION The variants of interest we identified in the NCs regulate a variety of neurological processes including cilia motility, cell metabolism, immune responses, and DNA damage repair and provide novel insights into the molecular pathogenesis of these extremely rare tumors.
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Affiliation(s)
- Sapna Khowal
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Dongyun Zhang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - William H Yong
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, 92868, USA
| | - Anthony P Heaney
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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Suga K, Imoto I, Ito H, Naruto T, Goji A, Osumi K, Tokaji N, Homma Y, Ono A, Ichihara Y, Shono M, Mori T, Urushihara M, Nakagawa R, Hayabuchi Y, Kagami S. Next-generation sequencing for the diagnosis of patients with congenital multiple anomalies and / or intellectual disabilities. THE JOURNAL OF MEDICAL INVESTIGATION 2020; 67:246-249. [PMID: 33148896 DOI: 10.2152/jmi.67.246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Background : In clinical practice, a large proportion of patients with multiple congenital anomalies and/or intellectual disabilities (MCA / ID) lacks a specific diagnosis. Recently, next-generation sequencing (NGS) has become an efficient strategy for genetic diagnosis of patients with MCA/ID. OBJECTIVE To review the utility of NGS for the diagnosis of patients with MCA / ID. METHOD Patients with MCA/ID were recruited between 2013 and 2017. Molecular diagnosis was performed using NGS-based targeted panel sequencing for 4,813 genes. Promising causative variants underwent confirmation by Sanger sequencing or chromosomal microarray. RESULTS Eighteen patients with MCA/ID were enrolled in this study. Of them, 8 cases (44%) were diagnosed by targeted panel sequencing. Most of diagnosed patients were able to receive better counseling and more appropriate medical management. CONCLUSION NGS-based targeted panel sequencing seems to be an effective testing strategy for diagnosis of patients with MCA/ID. J. Med. Invest. 67 : 246-249, August, 2020.
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Affiliation(s)
- Kenichi Suga
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Issei Imoto
- Department of Human Genetics, Graduate school of Biomedical Science, Tokushima University Graduate School, Tokushima, Japan.,Division of Molecular Genetics, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Cancer Genetics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiromichi Ito
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan.,Department of Special Needs Education, Graduate School of Education, Naruto University of Education, Naruto, Japan
| | - Takuya Naruto
- Department of Human Genetics, Graduate school of Biomedical Science, Tokushima University Graduate School, Tokushima, Japan
| | - Aya Goji
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Keita Osumi
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Narumi Tokaji
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Yukako Homma
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Akemi Ono
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Yuko Ichihara
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Miki Shono
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Tatsuo Mori
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Maki Urushihara
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | - Ryuji Nakagawa
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
| | | | - Shoji Kagami
- Department of Pediatrics, Tokushima University Hospital, Tokushima, Japan
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Gug C, Gorduza EV, Lăcătuşu A, Vaida MA, Bîrsăşteanu F, Puiu M, Stoicănescu D. CHARGE syndrome associated with de novo (I1460Rfs *15) frameshift mutation of CHD7 gene in a patient with arteria lusoria and horseshoe kidney. Exp Ther Med 2020; 20:479-485. [PMID: 32509017 PMCID: PMC7271729 DOI: 10.3892/etm.2020.8683] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/02/2020] [Indexed: 12/22/2022] Open
Abstract
CHARGE syndrome is an autosomal dominant condition caused by mutations in the chromodomain helicase DNA binding protein 7 (CHD7) gene. The present study reported on the case of a 16-month-old female with plurimalformative syndrome, whose etiology was identified by clinical whole-exome sequencing (WES) analysis. Clinical and follow-up assessments identified multiple craniofacial dysmorphisms, congenital defects and functional symptoms, including dysphagia and Marcus Gunn jaw winking synkinesis. Trio-WES analysis was performed for the patient and their parents and the presence of CHARGE syndrome was further indicated using single-molecule real-time sequencing. A de novo pathogenic variant, c.4379_4380del (p.Ile1460Argfs*15), was identified in exon 19 of the CHD7 gene, which resulted in a premature translational stop signal. Trio-WES analysis was used for further investigation, indicating that neither of the patient's parents had the mutation and confirming its de novo nature. To the best of our knowledge, the case of the present study was the first reported case of CHARGE syndrome in Romania with congenital defects including an aberrant right subclavian artery and a horseshoe kidney. CHARGE syndrome was diagnosed in the patient based on the pathogenic mutation in the CHD7 gene. To the best of our knowledge, the present case report is the first to suggest that the CHD7 gene variant is associated with CHARGE syndrome.
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Affiliation(s)
- Cristina Gug
- Department of Microscopic Morphology, Victor Babeş University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Eusebiu Vlad Gorduza
- Prenatal Diagnosis Department, Cuza Voda Obstetrics-Gynecology Clinical Hospital, 700038 Iasi, Romania.,Department of Medical Genetics, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adrian Lăcătuşu
- Department of Pediatrics, Victor Babeş University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Monica Adriana Vaida
- Department of Anatomy and Embryology, Victor Babeş University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Florin Bîrsăşteanu
- Department of Radiology and Medical Imaging, Victor Babeş University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Maria Puiu
- Department of Microscopic Morphology, Victor Babeş University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Dorina Stoicănescu
- Department of Microscopic Morphology, Victor Babeş University of Medicine and Pharmacy, 300041 Timisoara, Romania
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Ungaro C, Citrigno L, Trojsi F, Sprovieri T, Gentile G, Muglia M, Monsurrò MR, Tedeschi G, Cavallaro S, Conforti FL. ALS and CHARGE syndrome: a clinical and genetic study. Acta Neurol Belg 2018; 118:629-635. [PMID: 30317490 PMCID: PMC6244742 DOI: 10.1007/s13760-018-1029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/06/2018] [Indexed: 12/30/2022]
Abstract
Amyotrophic Lateral Sclerosis and CHARGE syndrome are complex neurological disorders, which never occurred together in the same family and, to date, no putative correlation between them has been described on PubMed Central. Due to our aim was to evaluate the presence of different genetic variants involved in these pathologies, we reported a clinical and genetic description of two sisters affected by these two different disorders. In the CHARGE patient, molecular analysis of the CHD7 gene revealed the c.8016G >A de novo variant in exon 37. The ALS patient had been screened negative for mutations in SOD1, TARDBP, FUS/TLS, C9orf72 and KIF5A genes. Anyway, targeted next generation sequencing analysis identified known and unknown genetic variations in 39 ALS-related genes: a total of 380 variants were reported, of which 194 in the ALS patient and 186 in the CHARGE patient. To date, although the results suggest that the occurrence of the two syndromes in the same family is co-incidental rather than based on a causative genetic variant, we could hypothesize that other factors might act as modulators in the pathogenesis of these different phenotypes.
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Affiliation(s)
- Carmine Ungaro
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Luigi Citrigno
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Francesca Trojsi
- Dipartimento di Scienze Mediche, Chirurgiche, Neurologiche, Metaboliche e dell'Invecchiamento, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Teresa Sprovieri
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Giulia Gentile
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Maria Muglia
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Maria Rosaria Monsurrò
- Dipartimento di Scienze Mediche, Chirurgiche, Neurologiche, Metaboliche e dell'Invecchiamento, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Gioacchino Tedeschi
- Dipartimento di Scienze Mediche, Chirurgiche, Neurologiche, Metaboliche e dell'Invecchiamento, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Sebastiano Cavallaro
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy
| | - Francesca Luisa Conforti
- Institute of Neurological Sciences (ISN), National Research Council, C.da Burga, Mangone, CS, Italy.
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Xu YP, Shi LP, Zhu J. Atypical CHARGE associated with a novel frameshift mutation of CHD7 in a Chinese neonatal patient. BMC Pediatr 2018; 18:203. [PMID: 29945602 PMCID: PMC6020284 DOI: 10.1186/s12887-018-1181-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/18/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND CHARGE syndrome is an autosomal dominant malformation disorder caused by heterozygous loss of function mutations in the chromatin remodeler CHD7, which has been estimated to occur in 1:10,000 births worldwide. It is a genetic disorder closely resembles other pattern of anomalies. Genetic testing should be pointed out as a useful method for clinical diagnosis. CASE PRESENTATION A female infant was the second child born to a 33-year-old, gravida 3, para 2 mother. The infant was born at 37 + 4 weeks of gestation with a birth weight of 2440 g (- 1.1 S.D.). Clinical examination showed atypical CHARGE syndrome, with choanal atresia, a heart defect, and sensorineural deafness. Genomic DNA was extracted from peripheral venous blood sample using molecular biological technique. We used the Illumina TruSigt One sequencing panel on the MiSeq next- generation sequencing (NGS) platform for mutation screening and found a novel frameshift mutation in chromodomain helicase DNA binding protein 7 (CHD7; c.4656dupT). This mutation results in a new reading frame ending in p.(Ile1553fs). At the first month of age, the patient had a posterior nostril plasty operation by nasal endoscope. At the second month of age, she had patent ductus arteriosus ligation surgery. At the 4th month of age, she was discharged from the hospital. CONCLUSIONS Our findings further reveal that patients should not be rejected for CHD7 mutational analysis even if they do not fulfill CHARGE syndrome Verloes criteria.
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Affiliation(s)
- Yan-Ping Xu
- NICU, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310053, China.
| | - Li-Ping Shi
- NICU, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310053, China
| | - Jiajun Zhu
- Department of Neonatology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
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Villate O, Ibarluzea N, Fraile-Bethencourt E, Valenzuela A, Velasco EA, Grozeva D, Raymond FL, Botella MP, Tejada MI. Functional Analyses of a Novel Splice Variant in the CHD7 Gene, Found by Next Generation Sequencing, Confirm Its Pathogenicity in a Spanish Patient and Diagnose Him with CHARGE Syndrome. Front Genet 2018; 9:7. [PMID: 29434620 PMCID: PMC5790995 DOI: 10.3389/fgene.2018.00007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/08/2018] [Indexed: 01/30/2023] Open
Abstract
Mutations in CHD7 have been shown to be a major cause of CHARGE syndrome, which presents many symptoms and features common to other syndromes making its diagnosis difficult. Next generation sequencing (NGS) of a panel of intellectual disability related genes was performed in an adult patient without molecular diagnosis. A splice donor variant in CHD7 (c.5665 + 1G > T) was identified. To study its potential pathogenicity, exons and flanking intronic sequences were amplified from patient DNA and cloned into the pSAD® splicing vector. HeLa cells were transfected with this construct and a wild-type minigene and functional analysis were performed. The construct with the c.5665 + 1G > T variant produced an aberrant transcript with an insert of 63 nucleotides of intron 28 creating a premature termination codon (TAG) 25 nucleotides downstream. This would lead to the insertion of 8 new amino acids and therefore a truncated 1896 amino acid protein. As a result of this, the patient was diagnosed with CHARGE syndrome. Functional analyses underline their usefulness for studying the pathogenicity of variants found by NGS and therefore its application to accurately diagnose patients.
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Affiliation(s)
- Olatz Villate
- Biocruces Health Research Institute, Barakaldo, Spain.,Molecular Genetics Laboratory, Genetics Service, Cruces University Hospital, Barakaldo, Spain
| | | | - Eugenia Fraile-Bethencourt
- Splicing and Cancer Laboratory, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Alberto Valenzuela
- Splicing and Cancer Laboratory, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Eladio A Velasco
- Splicing and Cancer Laboratory, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Detelina Grozeva
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - F L Raymond
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - María P Botella
- Department of Pediatrics, Araba University Hospital, Vitoria, Spain
| | - María-Isabel Tejada
- Biocruces Health Research Institute, Barakaldo, Spain.,Molecular Genetics Laboratory, Genetics Service, Cruces University Hospital, Barakaldo, Spain.,Clinical Group, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
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