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Dong MJ, Yang ZK, Yang J, Guo RQ, Xiao YY, Liu H. Gamma knife radiotherapy in a neurofibromatosis type 1 Chinese pedigrees with NF1 gene frameshift mutation: A case report. Medicine (Baltimore) 2022; 101:e29280. [PMID: 35801779 PMCID: PMC9259110 DOI: 10.1097/md.0000000000029280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
RATIONALE Neurofibromatosis type 1 (NF1) is a common autosomal dominant genetic disorder. NF1 is a multisystemic disease and its pathogenesis involves mutations in the NF1 gene on chromosome 17q11.2 causing RAS overactivation to stimulate abnormal cell proliferation. In this article, a Chinese family with neurofibromatosis type 1 was reported and the relationship between the phenotype and gene mutation was analyzed. PATIENT CONCERNS The patient was a 9-year-old-male child diagnosed with right eye exophthalmos combined with right eye glioma, optic edema, and peripheral visual field defect. There were multiple cafe-au-lait spots in the whole body of the child. His mother had multiple cafe-au-lait spots, and the eye examination showed no abnormalities. DIAGNOSIS The proband was diagnosed with NF1 and a heterozygous frameshift mutation (c. 6641delG p. Arg2214Asnfs*30) in the NF1 gene was identified, and his mother also carried the same pathogenic mutation. INTERVENTIONS To protect the vision of the right eye, he was treated with gamma knife radiotherapy. OUTCOMES After therapy, his fundus optic disc edema was decreased and the best corrected visual acuity of the right eye was increased. LESSONS Gene detection is helpful to diagnose the disease and guide the treatment. Gamma knife radiotherapy can preserve better neurological function.
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Affiliation(s)
- Meng-Jie Dong
- Department of Ophthalmology, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Research Center of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Center of Yunnan Province, Kunming, China
| | - Zhong-Kun Yang
- Department of Ophthalmology, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Research Center of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Center of Yunnan Province, Kunming, China
| | - Ji Yang
- Department of Ophthalmology, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Research Center of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Center of Yunnan Province, Kunming, China
| | - Rui-Qin Guo
- Department of Ophthalmology, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Research Center of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Center of Yunnan Province, Kunming, China
| | - Yu-Yuan Xiao
- Department of Ophthalmology, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Research Center of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Center of Yunnan Province, Kunming, China
| | - Hai Liu
- Department of Ophthalmology, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Research Center of Yunnan Province, Kunming, China
- The Eye Disease Clinical Medical Center of Yunnan Province, Kunming, China
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Application of Combined Long Amplicon Sequencing (CoLAS) for Genetic Analysis of Neurofibromatosis Type 1: A Pilot Study. Curr Issues Mol Biol 2021; 43:782-801. [PMID: 34449562 PMCID: PMC8929138 DOI: 10.3390/cimb43020057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/10/2021] [Accepted: 07/20/2021] [Indexed: 12/23/2022] Open
Abstract
Elaborate analyses of the status of gene mutations in neurofibromatosis type 1 (NF1) are still difficult nowadays due to the large gene sizes, broad mutation spectrum, and the various effects of mutations on mRNA splicing. These problems cannot be solved simply by sequencing the entire coding region using next-generation sequencing (NGS). We recently developed a new strategy, named combined long amplicon sequencing (CoLAS), which is a method for simultaneously analysing the whole genomic DNA region and, also, the full-length cDNA of the disease-causative gene with long-range PCR-based NGS. In this study, CoLAS was specifically arranged for NF1 genetic analysis, then applied to 20 patients (five previously reported and 15 newly recruited patients, including suspicious cases) for optimising the method and to verify its efficacy and benefits. Among new cases, CoLAS detected not only 10 mutations, including three unreported mutations and one mosaic mutation, but also various splicing abnormalities and allelic expression ratios quantitatively. In addition, heterozygous mapping by polymorphisms, including introns, showed copy number monitoring of the entire NF1 gene region was possible in the majority of patients tested. Moreover, it was shown that, when a chromosomal level microdeletion was suspected from heterozygous mapping, it could be detected directly by breakpoint-specific long PCR. In conclusion, CoLAS not simply detect the causative mutation but accurately elucidated the entire structure of the NF1 gene, its mRNA expression, and also the splicing status, which reinforces its high usefulness in the gene analysis of NF1.
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Togi S, Ura H, Niida Y. Optimization and Validation of Multimodular, Long-Range PCR-Based Next-Generation Sequencing Assays for Comprehensive Detection of Mutation in Tuberous Sclerosis Complex. J Mol Diagn 2021; 23:424-446. [PMID: 33486073 DOI: 10.1016/j.jmoldx.2020.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
The genetic diagnosis of tuberous sclerosis complex is difficult because of its broad spectrum of mutations. In addition to point mutations in coding regions, intragenic or chromosomal-level large deletions, deep intronic splicing mutations, and mosaic mutations represent a significant proportion of the mutations. In this study, multimodular, long-range PCR-based next-generation sequencing assays were optimized and validated using >100 samples with known TSC1 and TSC2 variants. Multiplex, long-range PCR covering the entire genomic region of both genes detected all 138 known variants; however, it also yielded false-positive results. Intragenic large deletions were detected with accurate breakpoint sequences. Chromosomal-level deletions were estimated by discordant allele segregation in the family and confirmed by DNA microarray. Deep intronic mutations were verified using a combination of long-range DNA PCR and full-length mRNA sequencing. DNA samples were mixed to simulate mosaic mutations, and most variants were detected but could not be distinguished from equivalently detected false-positive results. Repeated false-positive results were classified, and the strategy of selecting the common variants detected in the duplicate analysis and eliminating known false-positive results improved the sensitivity (85.2%) and positive predictive value (96.6%) of a 10% mosaic simulation. Long-range PCRbased next-generation sequencing is a highly versatile genetic test; however, confirmation tests remain necessary for clinical use because false-positive results cannot be completely eliminated from single experiments.
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Affiliation(s)
- Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University, Uchinada, Japan
| | - Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University, Uchinada, Japan
| | - Yo Niida
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Japan.
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Wang W, Qin W, Ge H, Kong X, Xie C, Tang Y, Li M. Clinical and molecular characteristics of thirty NF1 variants in Chinese patients with neurofibromatosis type 1. Mol Biol Rep 2019; 46:4349-4359. [PMID: 31201679 DOI: 10.1007/s11033-019-04888-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/15/2019] [Indexed: 01/29/2023]
Abstract
Neurofibromatosis type 1 (NF1) is a common autosomal dominant tumor-predisposition disorder that mainly impacts the nervous system and skin. Since the full clinical presentation of NF1 depends on age, it can be difficult to make an early and definite diagnosis in paediatric patients without family history who only exhibited multiple cafè-au-lait spots, highlighting the need for mutational analysis. A combination of techniques was conducted in 30 families with NF1, including multi-gene panels, direct sequencing, cDNA sequencing and multiplex ligation-dependent probe amplification. Thirty variants were identified in 36 patients from the 30 families, among which ten variants were novel. As a result, we confirmed that the combination of techniques were highly accurate and sensitive for identifying pathogenic variants in patients clinically suspected of having NF1, in particular, for patients who only present with multiple cafè-au-lait spots.
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Affiliation(s)
- Wen Wang
- Departments of Dermatology and Venereology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China
| | - Hongsong Ge
- Departments of Dermatology, Anhui Provincial Children's Hospital, Hefei, Anhui, China
| | | | - Chao Xie
- Department of Paediatrics, The First People's Hospital of Hefei, Hefei, Anhui, China
| | - Yunge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China.
| | - Ming Li
- Departments of Dermatology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Stella A, Lastella P, Loconte DC, Bukvic N, Varvara D, Patruno M, Bagnulo R, Lovaglio R, Bartolomeo N, Serio G, Resta N. Accurate Classification of NF1 Gene Variants in 84 Italian Patients with Neurofibromatosis Type 1. Genes (Basel) 2018; 9:genes9040216. [PMID: 29673180 PMCID: PMC5924558 DOI: 10.3390/genes9040216] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 11/16/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is one of the most common autosomal dominant genetic diseases. It is caused by mutations in the NF1 gene encoding for the large protein, neurofibromin. Genetic testing of NF1 is cumbersome because 50% of cases are sporadic, and there are no mutation hot spots. In addition, the most recognizable NF1 clinical features—café-au-lait (CALs) spots and axillary and/or inguinal freckling—appear early in childhood but are rather non-specific. Thus, the identification of causative variants is extremely important for early diagnosis, especially in paediatric patients. Here, we aimed to identify the underlying genetic defects in 72 index patients referred to our centre for NF1. Causative mutations were identified in 58 subjects, with 29 being novel changes. We evaluated missense and non-canonical splicing mutations with both protein and splicing prediction algorithms. The ratio of splicing mutations detected was higher than that reported in recent patients’ series and in the Human Gene Mutation Database (HGMD). After applying in silico predictive tools to 41 previously reported missense variants, we demonstrated that 46.3% of these putatively missense mutations were forecasted to alter splicing instead. Our data suggest that mutations affecting splicing can be frequently underscored if not analysed in depth. We confirm that hamartomas can be useful for diagnosing NF1 in children. Lisch nodules and cutaneous neurofibromas were more frequent in patients with frameshifting mutations. In conclusion, we demonstrated that comprehensive in silico analysis can be a highly specific method for predicting the nature of NF1 mutations and may help in assuring proper patient care.
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Affiliation(s)
- Alessandro Stella
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Patrizia Lastella
- Centro di Malattie Rare, Azienda Ospedaliero-Universitario Policlinico di Bari, 70124 Bari, Italy.
| | - Daria Carmela Loconte
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Nenad Bukvic
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Dora Varvara
- Azienda Ospedaliero-Universitario Policlinico di Bari, 70124 Bari, Italy.
| | - Margherita Patruno
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Rosanna Bagnulo
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Rosaura Lovaglio
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Nicola Bartolomeo
- Sezione di Igiene, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Gabriella Serio
- Sezione di Igiene, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
| | - Nicoletta Resta
- Laboratorio di Genetica Medica, Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari Aldo Moro, 70124 Bari, Italy.
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Zhu L, Zhang Y, Tong H, Shao M, Gu Y, Du X, Wang P, Shi L, Zhang L, Bi M, Wang X, Zhang G. Clinical and Molecular Characterization of NF1 Patients: Single-Center Experience of 32 Patients From China. Medicine (Baltimore) 2016; 95:e3043. [PMID: 26962827 PMCID: PMC4998908 DOI: 10.1097/md.0000000000003043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a hereditary disorder caused by mutations in the NF1 gene. Detecting mutation in NF1 is hindered by the gene's large size, the lack of mutation hotspots, and the presence of pseudogenes.Our goal was to establish a sensitive, feasible, and comparatively economical protocol to detect NF1 mutations using blood samples.We developed a method to screen patients for mutations. Thirty-two NF1 patients from 32 unrelated families and 120 unrelated population-match controls were investigated in this study. Specific primers were designed for NF1 to avoid pseudogenes. NF1 mutations were detected by sequencing at the deoxyribonucleic acid (DNA) and complementary DNA (cDNA) levels, and multiplex ligation-dependent probe amplification (MLPA) and familial segregation analyses were used.Forty-four specific primers designed according to the NF1 structure were successfully used for polymerase chain reaction (PCR) and DNA sequencing, which was more feasible and useful than cDNA sequencing. Thirty distinct NF1 mutations were identified in 32 patients. Thirteen mutations were novel and most were frameshift mutations (33.3%). Mutations were detected at a rate of 93.8%.Our study suggests that this sensitive, feasible, and comparatively economical protocol is effective for the detection of NF1 mutations.
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Affiliation(s)
- Lude Zhu
- From the Institute of Photomedicine, Shanghai Skin Disease Hospital, Tongji University School of Medicine (LZ, YZ, PW, LS, LZ, XW, GZ); Department of General Surgery, Zhong Shan Hospital, Fu Dan University (HT), Shanghai; and Department of Dermatology, Nanjing Medical University, Affiliated Wuxi People's Hospital, Wuxi, Jiangsu (MS, YG, XD, MB), China
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