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Perez-Becerril C, Burghel GJ, Hartley C, Rowlands CF, Evans DG, Smith MJ. Improved sensitivity for detection of pathogenic variants in familial NF2-related schwannomatosis. J Med Genet 2024; 61:452-458. [PMID: 38302265 DOI: 10.1136/jmg-2023-109586] [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: 08/19/2023] [Accepted: 12/07/2023] [Indexed: 02/03/2024]
Abstract
PURPOSE To determine the impact of additional genetic screening techniques on the rate of detection of pathogenic variants leading to familial NF2-related schwannomatosis. METHODS We conducted genetic screening of a cohort of 168 second-generation individuals meeting the clinical criteria for NF2-related schwannomatosis. In addition to the current clinical screening techniques, targeted next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification analysis, we applied additional genetic screening techniques, including karyotype and RNA analysis. For characterisation of a complex structural variant, we also performed long-read sequencing analysis. RESULTS Additional genetic analysis resulted in increased sensitivity of detection of pathogenic variants from 87% to 95% in our second-generation NF2-related schwannomatosis cohort. A number of pathogenic variants identified through extended analysis had been previously observed after NGS analysis but had been overlooked or classified as variants of uncertain significance. CONCLUSION Our study indicates there is added value in performing additional genetic analysis for detection of pathogenic variants that are difficult to identify with current clinical genetic screening methods. In particular, RNA analysis is valuable for accurate classification of non-canonical splicing variants. Karyotype analysis and whole genome sequencing analysis are of particular value for identification of large and/or complex structural variants, with additional advantages in the use of long-read sequencing techniques.
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Affiliation(s)
- Cristina Perez-Becerril
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Claire Hartley
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Charles F Rowlands
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Miriam J Smith
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, UK
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2
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Mudau MM, Dillon B, Smal C, Feben C, Honey E, Carstens N, Krause A. Mutation analysis and clinical profile of South African patients with Neurofibromatosis type 1 (NF1) phenotype. Front Genet 2024; 15:1331278. [PMID: 38596211 PMCID: PMC11002079 DOI: 10.3389/fgene.2024.1331278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic condition with complete age-dependent penetrance, variable expressivity and a global prevalence of ∼1/3,000. It is characteriszed by numerous café-au-lait macules, skin freckling in the inguinal or axillary regions, Lisch nodules of the iris, optic gliomas, neurofibromas, and tumour predisposition. The diagnostic testing strategy for NF1 includes testing for DNA single nucleotide variants (SNVs), copy number variants (CNVs) as well as RNA analysis for deep intronic and splice variants, which can cumulatively identify the causative variant in 95% of patients. In the present study, NF1 patients were screened using a next-generation sequencing (NGS) assay targeting NF1 exons and intron/exon boundaries for SNV and NF1 multiple ligation-dependent probe amplification (MLPA) analysis for CNV detection. Twenty-six unrelated Southern African patients clinically suspected of having NF1, based on the clinical diagnostic criteria developed by the National Institute of Health (NIH), were included in the current study. A detection rate of 58% (15/26) was obtained, with SNVs identified in 80% (12/15) using a targeted gene panel and NF1 gene deletion in 20% (3/15) identified using MLPA. Ten patients (38%) had no variants identified, although they met NF1 diagnostic criteria. One VUS was identified in this study in a patient that met NF1 diagnostic criteria, however there was no sufficient information to classify variant as pathogenic. The clinical features of Southern African patients with NF1 are similar to that of the known NF1 phenotype, with the exception of a lower frequency of plexiform neurofibromas and a higher frequency of developmental/intellectual disability compared to other cohorts. This is the first clinical and molecular characterisation of a Southern African ancestry NF1 cohort using both next-generation sequencing and MLPA analysis. A significant number of patients remained without a diagnosis following DNA-level testing. The current study offers a potential molecular testing strategy for our low resource environment that could benefit a significant proportion of patients who previously only received a clinical diagnosis without molecular confirmation.
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Affiliation(s)
- Maria Mabyalwa Mudau
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bronwyn Dillon
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clarice Smal
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engela Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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3
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Sargen MR, Kim J, Potjer TP, Velthuizen ME, Martir-Negron AE, Odia Y, Helgadottir H, Hatton JN, Haley JS, Thone G, Widemann BC, Gross AM, Yohe ME, Kaplan RN, Shern JF, Sundby RT, Astiazaran-Symonds E, Yang XR, Carey DJ, Tucker MA, Stewart DR, Goldstein AM. Estimated Prevalence, Tumor Spectrum, and Neurofibromatosis Type 1-Like Phenotype of CDKN2A-Related Melanoma-Astrocytoma Syndrome. JAMA Dermatol 2023; 159:1112-1118. [PMID: 37585199 PMCID: PMC10433137 DOI: 10.1001/jamadermatol.2023.2621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/14/2023] [Indexed: 08/17/2023]
Abstract
Importance Knowledge about the prevalence and tumor types of CDKN2A-related melanoma-astrocytoma syndrome (MAS) is limited and could improve disease recognition. Objective To estimate the prevalence and describe the tumor types of MAS. Design, Setting, and Participants This retrospective cohort study analyzed all available MAS cases from medical centers in the US (2 sites) and Europe (2 sites) and from biomedical population genomic databases (UK Biobank [United Kingdom], Geisinger MyCode [US]) between January 1, 1976, and December 31, 2020. Patients with MAS with CDKN2A germline pathogenic variants and 1 or more neural tumors were included. Data were analyzed from June 1, 2022, to January 31, 2023. Main Outcomes and Measures Disease prevalence and tumor frequency. Results Prevalence of MAS ranged from 1 in 170 503 (n = 1 case; 95% CI, 1:30 098-1:965 887) in Geisinger MyCode (n = 170 503; mean [SD] age, 58.9 [19.1] years; 60.6% women; 96.2% White) to 1 in 39 149 (n = 12 cases; 95% CI, 1:22 396-1:68 434) in UK Biobank (n = 469 789; mean [SD] age, 70.0 [8.0] years; 54.2% women; 94.8% White). Among UK Biobank patients with MAS (n = 12) identified using an unbiased genomic ascertainment approach, brain neoplasms (4 of 12, 33%; 1 glioblastoma, 1 gliosarcoma, 1 astrocytoma, 1 unspecified type) and schwannomas (3 of 12, 25%) were the most common malignant and benign neural tumors, while cutaneous melanoma (2 of 12, 17%) and head and neck squamous cell carcinoma (2 of 12, 17%) were the most common nonneural malignant neoplasms. In a separate case series of 14 patients with MAS from the US and Europe, brain neoplasms (4 of 14, 29%; 2 glioblastomas, 2 unspecified type) and malignant peripheral nerve sheath tumor (2 of 14, 14%) were the most common neural cancers, while cutaneous melanoma (4 of 14, 29%) and sarcomas (2 of 14, 14%; 1 liposarcoma, 1 unspecified type) were the most common nonneural cancers. Cutaneous neurofibromas (7 of 14, 50%) and schwannomas (2 of 14, 14%) were also common. In 1 US family, a father and son with MAS had clinical diagnoses of neurofibromatosis type 1 (NF1). Genetic testing of the son detected a pathogenic CDKN2A splicing variant (c.151-1G>C) and was negative for NF1 genetic alterations. In UK Biobank, 2 in 150 (1.3%) individuals with clinical NF1 diagnoses had likely pathogenic variants in CDKN2A, including 1 individual with no detected variants in the NF1 gene. Conclusions and Relevance This cohort study estimates the prevalence and describes the tumors of MAS. Additional studies are needed in genetically diverse populations to further define population prevalence and disease phenotypes.
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Affiliation(s)
- Michael R. Sargen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Thomas P. Potjer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Mary E. Velthuizen
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Yazmin Odia
- Miami Cancer Institute, Baptist Health South Florida, Miami
| | - Hildur Helgadottir
- Department of Oncology and Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jessica N. Hatton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Jeremy S. Haley
- Department of Genomic Health, Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Gretchen Thone
- Department of Genomic Health, Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Brigitte C. Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Andrea M. Gross
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Marielle E. Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, Frederick, Maryland
| | - Rosandra N. Kaplan
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jack F. Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - R. Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - David J. Carey
- Department of Genomic Health, Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Margaret A. Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Douglas R. Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
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Wang W, Li X, Qin X, Miao Y, Zhang Y, Li S, Yao R, Yang Y, Yu L, Zhu H, Song L, Mao S, Wang X, Chen J, Feng H, Li Y. Germline Neurofibromin 1 mutation enhances the anti-tumour immune response and decreases juvenile myelomonocytic leukaemia tumourigenicity. Br J Haematol 2023. [PMID: 37144690 DOI: 10.1111/bjh.18851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/10/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023]
Abstract
Juvenile myelomonocytic leukaemia (JMML) is an aggressive paediatric leukaemia characterized by mutations in five canonical RAS pathway genes, including the NF1 gene. JMML is driven by germline NF1 gene mutations, with additional somatic aberrations resulting in the NF1 biallelic inactivation, leading to disease progression. Germline mutations in the NF1 gene alone primarily cause benign neurofibromatosis type 1 (NF1) tumours rather than malignant JMML, yet the underlying mechanism remains unclear. Here, we demonstrate that with reduced NF1 gene dose, immune cells are promoted in anti-tumour immune response. Comparing the biological properties of JMML and NF1 patients, we found that not only JMML but also NF1 patients driven by NF1 mutations could increase monocytes generation. But monocytes cannot further malignant development in NF1 patients. Utilizing haematopoietic and macrophage differentiation from iPSCs, we revealed that NF1 mutations or knockout (KO) recapitulated the classical haematopoietic pathological features of JMML with reduced NF1 gene dose. NF1 mutations or KO promoted the proliferation and immune function of NK cells and iMacs derived from iPSCs. Moreover, NF1-mutated iNKs had a high capacity to kill NF1-KO iMacs. NF1-mutated or KO iNKs administration delayed leukaemia progression in a xenograft animal model. Our findings demonstrate that germline NF1 mutations alone cannot directly drive JMML development and suggest a potential cell immunotherapy for JMML patients.
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Affiliation(s)
- Wanqiao Wang
- Pediatric Translational Medicine Institute, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Key Laboratory of Pediatric Hematology & Oncology of China Ministry of Health, Shanghai, China
| | - Xin Li
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai, China
| | - Xia Qin
- Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Yan Miao
- Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Yingwen Zhang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanshan Li
- Pediatric Translational Medicine Institute, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Key Laboratory of Pediatric Hematology & Oncology of China Ministry of Health, Shanghai, China
| | - Ruen Yao
- Department of Medical Genetics, Shanghai Children's Medical Center, Shanghai, China
| | - Yi Yang
- Pediatric Translational Medicine Institute, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Key Laboratory of Pediatric Hematology & Oncology of China Ministry of Health, Shanghai, China
| | - Lisha Yu
- Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Hua Zhu
- Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Lili Song
- Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Shengqiao Mao
- Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai, China
| | - Jing Chen
- Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Haizhong Feng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanxin Li
- Pediatric Translational Medicine Institute, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Key Laboratory of Pediatric Hematology & Oncology of China Ministry of Health, Shanghai, China
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5
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Alesi V, Genovese S, Lepri FR, Catino G, Loddo S, Orlando V, Di Tommaso S, Morgia A, Martucci L, Di Donato M, Digilio MC, Dallapiccola B, Novelli A, Capolino R. Deep Intronic LINE-1 Insertions in NF1: Expanding the Spectrum of Neurofibromatosis Type 1-Associated Rearrangements. Biomolecules 2023; 13:biom13050725. [PMID: 37238595 DOI: 10.3390/biom13050725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Neurofibromatosis type 1 is an autosomal-dominant condition caused by NF1 gene inactivation. Clinical diagnosis is corroborated by genetic tests on gDNA and cDNA, which are inconclusive in approximately 3-5% of cases. Genomic DNA approaches may overlook splicing-affecting intronic variants and structural rearrangements, especially in regions enriched in repetitive sequences. On the other hand, while cDNA-based methods provide direct information about the effect of a variant on gene transcription, they are hampered by non-sense-mediated mRNA decay and skewed or monoallelic expression. Moreover, analyses on gene transcripts in some patients do not allow tracing back to the causative event, which is crucial for addressing genetic counselling, prenatal monitoring, and developing targeted therapies. We report on a familial NF1, caused by an insertion of a partial LINE-1 element inside intron 15, leading to exon 15 skipping. Only a few cases of LINE-1 insertion have been reported so far, hampering gDNA studies because of their size. Often, they result in exon skipping, and their recognition of cDNA may be difficult. A combined approach, based on Optical Genome Mapping, WGS, and cDNA studies, enabled us to detect the LINE-1 insertion and test its effects. Our results improve knowledge of the NF1 mutational spectrum and highlight the importance of custom-built approaches in undiagnosed patients.
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Affiliation(s)
- Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Francesca Romana Lepri
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Sara Loddo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Valeria Orlando
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Silvia Di Tommaso
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Alessandra Morgia
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Licia Martucci
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Maddalena Di Donato
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Maria Cristina Digilio
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy
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6
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Núñez-Moreno G, Tamayo A, Ruiz-Sánchez C, Cortón M, Mínguez P. VIsoQLR: an interactive tool for the detection, quantification and fine-tuning of isoforms in selected genes using long-read sequencing. Hum Genet 2023; 142:495-506. [PMID: 36881176 DOI: 10.1007/s00439-023-02539-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
DNA variants altering the pre-mRNA splicing process represent an underestimated cause of human genetic diseases. Their association with disease traits should be confirmed using functional assays from patient cell lines or alternative models to detect aberrant mRNAs. Long-read sequencing is a suitable technique to identify and quantify mRNA isoforms. Available isoform detection and/or quantification tools are generally designed for the whole transcriptome analysis. However experiments focusing on genes of interest need more precise data fine-tuning and visualization tools.Here we describe VIsoQLR, an interactive analyzer, viewer and editor for the semi-automated identification and quantification of known and novel isoforms using long-read sequencing data. VIsoQLR is tailored to thoroughly analyze mRNA expression in splicing assays of selected genes. Our tool takes sequences aligned to a reference, and for each gene, it defines consensus splice sites and quantifies isoforms. VIsoQLR introduces features to edit the splice sites through dynamic and interactive graphics and tables, allowing accurate manual curation. Known isoforms detected by other methods can also be imported as references for comparison. A benchmark against two other popular transcriptome-based tools shows VIsoQLR accurate performance on both detection and quantification of isoforms. Here, we present VIsoQLR principles and features and its applicability in a case study example using nanopore-based long-read sequencing. VIsoQLR is available at https://github.com/TBLabFJD/VIsoQLR .
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Affiliation(s)
- Gonzalo Núñez-Moreno
- Department of Genetics and Genomics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.
- Bioinformatics Unit, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
| | - Alejandra Tamayo
- Department of Genetics and Genomics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, Science and Technology Campus, University of Alcalá, 28871, Alcalá de Henares, Spain
| | - Carolina Ruiz-Sánchez
- Department of Genetics and Genomics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Marta Cortón
- Department of Genetics and Genomics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics and Genomics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Bioinformatics Unit, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
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7
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Contribution of whole genome sequencing in the molecular diagnosis of mosaic partial deletion of the NF1 gene in neurofibromatosis type 1. Hum Genet 2023; 142:1-9. [PMID: 35941319 DOI: 10.1007/s00439-022-02476-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023]
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant disease with complete penetrance but highly variable expressivity. In most patients, Next Generation Sequencing (NGS) technologies allow the identification of a loss-of-function pathogenic variant in the NF1 gene, a negative regulator of the RAS-MAPK pathway. We describe the 5-year diagnosis wandering of a patient with a clear NF1 clinical diagnosis, but no molecular diagnosis using standard molecular technologies. The patient presented with a typical NF1 phenotype but NF1 targeted NGS, NF1 transcript analysis, MLPA, and array comparative genomic hybridization failed to reveal a genetic aberration. After 5 years of unsuccessful investigations, trio WGS finally identified a de novo mosaic (VAF ~ 14%) 24.6 kb germline deletion encompassing the promoter and first exon of NF1. This case report illustrates the relevance of WGS to detect structural variants including copy number variants that would be missed by alternative approaches. The identification of the causal pathogenic variant allowed a tailored genetic counseling with a targeted non-invasive prenatal diagnosis by detecting the deletion in plasmatic cell-free DNA from the proband's pregnant partner. This report clearly highlights the need to make WGS a clinically accessible test, offering a tremendous opportunity to identify a molecular diagnosis for otherwise unsolved cases.
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8
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Douben HCW, Nellist M, van Unen L, Elfferich P, Kasteleijn E, Hoogeveen-Westerveld M, Louwen J, van Veghel-Plandsoen M, de Valk W, Saris JJ, Hendriks F, Korpershoek E, Hoefsloot LH, van Vliet M, van Bever Y, van de Laar I, Aten E, Lachmeijer AMA, Taal W, van den Bersselaar L, Schuurmans J, Oostenbrink R, van Minkelen R, van Ierland Y, van Ham TJ. High-yield identification of pathogenic NF1 variants by skin fibroblast transcriptome screening after apparently normal diagnostic DNA testing. Hum Mutat 2022; 43:2130-2140. [PMID: 36251260 PMCID: PMC10099955 DOI: 10.1002/humu.24487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023]
Abstract
Neurofibromatosis type 1 (NF1) is caused by inactivating mutations in NF1. Due to the size, complexity, and high mutation rate at the NF1 locus, the identification of causative variants can be challenging. To obtain a molecular diagnosis in 15 individuals meeting diagnostic criteria for NF1, we performed transcriptome analysis (RNA-seq) on RNA obtained from cultured skin fibroblasts. In each case, routine molecular DNA diagnostics had failed to identify a disease-causing variant in NF1. A pathogenic variant or abnormal mRNA splicing was identified in 13 cases: 6 deep intronic variants and 2 transposon insertions causing noncanonical splicing, 3 postzygotic changes, 1 branch point mutation and, in 1 case, abnormal splicing for which the responsible DNA change remains to be identified. These findings helped resolve the molecular findings for an additional 17 individuals in multiple families with NF1, demonstrating the utility of skin-fibroblast-based transcriptome analysis for molecular diagnostics. RNA-seq improves mutation detection in NF1 and provides a powerful complementary approach to DNA-based methods. Importantly, our approach is applicable to other genetic disorders, particularly those caused by a wide variety of variants in a limited number of genes and specifically for individuals in whom routine molecular DNA diagnostics did not identify the causative variant.
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Affiliation(s)
- Hannie C W Douben
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leontine van Unen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter Elfferich
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esmee Kasteleijn
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Jesse Louwen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Walter de Valk
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Femke Hendriks
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esther Korpershoek
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Margreethe van Vliet
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ingrid van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Augusta M A Lachmeijer
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Walter Taal
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands.,Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lisa van den Bersselaar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Juliette Schuurmans
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rianne Oostenbrink
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands.,Department of General Pediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Yvette van Ierland
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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9
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Alesi V, Lepri FR, Dentici ML, Genovese S, Sallicandro E, Bejo K, Dallapiccola B, Capolino R, Novelli A, Digilio MC. Intragenic inversions in NF1 gene as pathogenic mechanism in neurofibromatosis type 1. Eur J Hum Genet 2022; 30:1239-1243. [PMID: 35879407 PMCID: PMC9626576 DOI: 10.1038/s41431-022-01153-3] [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: 09/24/2021] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Neurofibromatosis type 1 (NF1), an autosomal dominant disorder characterized by skin pigmentary lesions and multiple cutaneous neurofibromas, is caused by neurofibromin 1 (NF1) loss of function variants. Currently, a molecular diagnosis is frequently established using a multistep protocol based on cDNA and gDNA sequence analysis and/or Multiplex Ligation-dependent Probe Amplification (MLPA) assay on genomic DNA, providing an overall detection rate of about 95-97%. The small proportion of clinically diagnosed patients, which at present do not obtain a molecular confirmation likely are mosaic, as their pathogenic variant may remain undetected due to low sensitivity of low coverage NGS approaches, or they may carry a type of pathogenic variant refractory to currently used technologies. Here, we report two unrelated patients presenting with two different inversions that disrupt the NF1 coding sequence, resulting in an NF1 phenotype. In one subject, the inversion was associated with microdeletions spanning a few NF1 exons at both breakpoints, while in the other the rearrangement did not cause exon loss, thus testing negative by MLPA assay. Considering the high proportion of repeated regions within the NF1 sequence, we propose that intragenic structural rearrangements should be considered as possible pathogenic mechanisms in patients fulfilling the NIH diagnostic criteria of NF1 but lacking of molecular confirmation and in patients with NF1 intragenic microdeletions.
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Affiliation(s)
- Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy.
| | - Francesca Romana Lepri
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Ester Sallicandro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Kristel Bejo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
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10
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Ellingford JM, Ahn JW, Bagnall RD, Baralle D, Barton S, Campbell C, Downes K, Ellard S, Duff-Farrier C, FitzPatrick DR, Greally JM, Ingles J, Krishnan N, Lord J, Martin HC, Newman WG, O’Donnell-Luria A, Ramsden SC, Rehm HL, Richardson E, Singer-Berk M, Taylor JC, Williams M, Wood JC, Wright CF, Harrison SM, Whiffin N. Recommendations for clinical interpretation of variants found in non-coding regions of the genome. Genome Med 2022; 14:73. [PMID: 35850704 PMCID: PMC9295495 DOI: 10.1186/s13073-022-01073-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/16/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. METHODS We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. RESULTS We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. CONCLUSIONS These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.
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Affiliation(s)
- Jamie M. Ellingford
- grid.5379.80000000121662407Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT UK ,grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK ,grid.498322.6Genomics England, London, UK
| | - Joo Wook Ahn
- grid.24029.3d0000 0004 0383 8386Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Richard D. Bagnall
- grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia
| | - Diana Baralle
- grid.5491.90000 0004 1936 9297School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK ,grid.430506.40000 0004 0465 4079Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Stephanie Barton
- grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Chris Campbell
- grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Kate Downes
- grid.24029.3d0000 0004 0383 8386Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Sian Ellard
- grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK ,grid.419309.60000 0004 0495 6261South West Genomic Laboratory Hub, Exeter Genomic Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Celia Duff-Farrier
- grid.418484.50000 0004 0380 7221South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - David R. FitzPatrick
- grid.417068.c0000 0004 0624 9907MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John M. Greally
- grid.251993.50000000121791997Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY USA
| | - Jodie Ingles
- grid.1005.40000 0004 4902 0432Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Neesha Krishnan
- grid.1005.40000 0004 4902 0432Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Jenny Lord
- grid.5491.90000 0004 1936 9297School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hilary C. Martin
- grid.10306.340000 0004 0606 5382Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - William G. Newman
- grid.5379.80000000121662407Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT UK ,grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Anne O’Donnell-Luria
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.2515.30000 0004 0378 8438Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA USA ,grid.32224.350000 0004 0386 9924Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Simon C. Ramsden
- grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Heidi L. Rehm
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Ebony Richardson
- grid.1005.40000 0004 4902 0432Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Moriel Singer-Berk
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Jenny C. Taylor
- grid.4991.50000 0004 1936 8948National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK ,grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Maggie Williams
- grid.418484.50000 0004 0380 7221South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Jordan C. Wood
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Caroline F. Wright
- grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Steven M. Harrison
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA USA
| | - Nicola Whiffin
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
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11
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Genotype-Phenotype Correlations in Neurofibromatosis Type 1: Identification of Novel and Recurrent NF1 Gene Variants and Correlations with Neurocognitive Phenotype. Genes (Basel) 2022; 13:genes13071130. [PMID: 35885913 PMCID: PMC9316015 DOI: 10.3390/genes13071130] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 02/01/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is one of the most common genetic tumor predisposition syndrome, caused by mutations in the NF1. To date, few genotype-phenotype correlations have been discerned in NF1, due to a highly variable clinical presentation. We aimed to study the molecular spectrum of NF1 and genotype-phenotype correlations in a monocentric study cohort of 85 NF1 patients (20 relatives, 65 sporadic cases). Clinical data were collected at the time of the mutation analysis and reviewed for accuracy in this investigation. An internal phenotypic categorization was applied. The 94% of the patients enrolled showed a severe phenotype with at least one systemic complication and a wide range of associated malignancies. Spine deformities were the most common complications in this cohort. We also reported 66 different NF1 mutations, of which 7 are novel mutations. Correlation analysis identified a slight significant inverse correlation between age at diagnosis and delayed acquisition of psychomotor skills with residual multi-domain cognitive impairment. Odds ratio with 95% confidence interval showed a higher prevalence of learning disabilities in patients carrying frameshift mutations. Overall, our results aim to offer an interesting contribution to studies on the genotype–phenotype of NF1 and in genetic management and counselling.
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12
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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13
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Case series of congenital pseudarthrosis of the tibia unfulfilling neurofibromatosis type 1 diagnosis: 21% with somatic NF1 haploinsufficiency in the periosteum. Hum Genet 2022; 141:1371-1383. [DOI: 10.1007/s00439-021-02429-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/29/2021] [Indexed: 12/17/2022]
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14
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Kehrer-Sawatzki H, Cooper DN. Challenges in the diagnosis of neurofibromatosis type 1 (NF1) in young children facilitated by means of revised diagnostic criteria including genetic testing for pathogenic NF1 gene variants. Hum Genet 2021; 141:177-191. [PMID: 34928431 PMCID: PMC8807470 DOI: 10.1007/s00439-021-02410-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/03/2021] [Indexed: 12/21/2022]
Abstract
Neurofibromatosis type 1 (NF1) is the most frequent disorder associated with multiple café-au-lait macules (CALM) which may either be present at birth or appear during the first year of life. Other NF1-associated features such as skin-fold freckling and Lisch nodules occur later during childhood whereas dermal neurofibromas are rare in young children and usually only arise during early adulthood. The NIH clinical diagnostic criteria for NF1, established in 1988, include the most common NF1-associated features. Since many of these features are age-dependent, arriving at a definitive diagnosis of NF1 by employing these criteria may not be possible in infancy if CALM are the only clinical feature evident. Indeed, approximately 46% of patients who are diagnosed with NF1 later in life do not meet the NIH diagnostic criteria by the age of 1 year. Further, the 1988 diagnostic criteria for NF1 are not specific enough to distinguish NF1 from other related disorders such as Legius syndrome. In this review, we outline the challenges faced in diagnosing NF1 in young children, and evaluate the utility of the recently revised (2021) diagnostic criteria for NF1, which include the presence of pathogenic variants in the NF1 gene and choroidal anomalies, for achieving an early and accurate diagnosis.
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Affiliation(s)
- Hildegard Kehrer-Sawatzki
- Institute of Human Genetics, University Hospital Ulm, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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15
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Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq. NPJ Genom Med 2021; 6:95. [PMID: 34782607 PMCID: PMC8593033 DOI: 10.1038/s41525-021-00258-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/15/2021] [Indexed: 11/08/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is caused by loss-of-function variants in the NF1 gene. Approximately 10% of these variants affect RNA splicing and are either missed by conventional DNA diagnostics or are misinterpreted by in silico splicing predictions. Therefore, a targeted RNAseq-based approach was designed to detect pathogenic RNA splicing and associated pathogenic DNA variants. For this method RNA was extracted from lymphocytes, followed by targeted RNAseq. Next, an in-house developed tool (QURNAs) was used to calculate the enrichment score (ERS) for each splicing event. This method was thoroughly tested using two different patient cohorts with known pathogenic splice-variants in NF1. In both cohorts all 56 normal reference transcript exon splice junctions, 24 previously described and 45 novel non-reference splicing events were detected. Additionally, all expected pathogenic splice-variants were detected. Eleven patients with NF1 symptoms were subsequently tested, three of which have a known NF1 DNA variant with a putative effect on RNA splicing. This effect could be confirmed for all 3. The other eight patients were previously without any molecular confirmation of their NF1-diagnosis. A deep-intronic pathogenic splice variant could now be identified for two of them (25%). These results suggest that targeted RNAseq can be successfully used to detect pathogenic RNA splicing variants in NF1.
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16
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Rubinstein CD, McLean DT, Lehman BP, Meudt JJ, Schomberg DT, Krentz KJ, Reichert JL, Meyer MB, Adams M, Konsitzke CM, Shanmuganayagam D. Assessment of Mosaicism and Detection of Cryptic Alleles in CRISPR/Cas9-Engineered Neurofibromatosis Type 1 and TP53 Mutant Porcine Models Reveals Overlooked Challenges in Precision Modeling of Human Diseases. Front Genet 2021; 12:721045. [PMID: 34630515 PMCID: PMC8495252 DOI: 10.3389/fgene.2021.721045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/18/2021] [Indexed: 12/20/2022] Open
Abstract
Genome editing in pigs has been made efficient, practical, and economically viable by the CRISPR/Cas9 platform, representing a promising new era in translational modeling of human disease for research and preclinical development of therapies and devices. Porcine embryo microinjection provides a universally available, efficient option over somatic-cell nuclear transfer, but requires that critical considerations be made in genotypic validation of the models that routinely go unaddressed. Accurate validation of genotypes is especially important when modeling genetic disorders, such as neurofibromatosis type 1 (NF1) that exhibits complex genotype–phenotypic relationships. NF1, an autosomal dominant disorder, is particularly hard to model as it manifests very differently across patients, and even within families, with over 3,000 disease-associated mutations of the neurofibromin 1 (NF1) gene identified. The precise nature of the mutations plays a role in the complex phenotypic presentation of the disorder that includes benign and malignant peripheral and central nervous system tumors, a variety of motor deficits and debilitating cognitive impairments and musculoskeletal, cardiovascular, and gastrointestinal disorders. NF1 can also often involve mutations in passenger genes such as TP53. In this manuscript, we describe the creation of three novel porcine models of NF1 and a model additionally harboring a mutation in TP53 by embryo microinjection of CRISPR/Cas9. We present the challenges encountered in validation of genotypes and the methodological strategies developed to counter the hurdles. We present simple options for quantifying level of mosaicism: a quantitative method (targeted amplicon sequencing) for small edits such as SNPs and indels and a semiquantitative method (competitive PCR) for large edits. Characterization of mosaicism allowed for strategic selection of founder pigs for rapid, economical expansion of genetically defined lines. We also present commonly observed unexpected DNA repair products (i.e., structural variants or cryptic alleles) that are refractory to PCR amplification and thus evade detection. We present the use of copy number variance assays to overcome hurdles in detecting cryptic alleles. The report provides a framework for genotypic validation of porcine models created by embryo microinjection and the expansion of lines in an efficient manner.
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Affiliation(s)
| | - Dalton T McLean
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Brent P Lehman
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jennifer J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Dominic T Schomberg
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Kathy J Krentz
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jamie L Reichert
- Swine Research and Teaching Center, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Charles M Konsitzke
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States.,Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
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17
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Ece Solmaz A, Isik E, Atik T, Ozkinay F, Onay H. Mutation spectrum of the NF1 gene and genotype-phenotype correlations in Turkish patients: Seventeen novel pathogenic variants. Clin Neurol Neurosurg 2021; 208:106884. [PMID: 34418705 DOI: 10.1016/j.clineuro.2021.106884] [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: 11/26/2020] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVE Neurofibromatosis type 1 is one of the most common autosomal dominant diseases caused by heterozygous mutation in the NF1 gene. Wide spectrum of NF1-related clinical manifestations and mutation distribution makes genetic counselling difficult. METHODS The study enrolled 58 unrelated Turkish patients with clinically suspected NF1 referred to the Department of Medical Genetics. Individuals were eligible if they 1) met at least two of the main National Institutes of Health criteria or 2) had multiple café-au-lait macules as a child. RESULTS Fourty-one different disease-causing variants were identified in 42 (72.4%) individuals, including 17 novel variants. Twenty-four (58.2%) of the NF1 patients had de novo variants. Café-au-lait macules were observed in all patients (100%). Intracranial hamartoma was the second most common phenotype, found in 52.3% (22/42) of the patients. Other common manifestations were neurofibromas (35.7%), axillary or inguinal freckling (28.5%), and Lisch nodules (28.5%). Additionally, one patient had intra-abdominal malignant peripheral nerve sheath tumours and another patient underwent surgery for serous papillary ovarian cancer. CONCLUSION In conclusion, this study is one of the largest studies from Turkey to investigate the NF1 mutation spectrum and genotype-phenotype correlations.
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Affiliation(s)
- Asli Ece Solmaz
- Ege University Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey.
| | - Esra Isik
- University Faculty of Medicine, Department of Pediatrics, Division of Pediatric Genetics, Izmir, Turkey
| | - Tahir Atik
- University Faculty of Medicine, Department of Pediatrics, Division of Pediatric Genetics, Izmir, Turkey
| | - Ferda Ozkinay
- University Faculty of Medicine, Department of Pediatrics, Division of Pediatric Genetics, Izmir, Turkey
| | - Huseyin Onay
- Ege University Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
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18
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Perez-Becerril C, Evans DG, Smith MJ. Pathogenic noncoding variants in the neurofibromatosis and schwannomatosis predisposition genes. Hum Mutat 2021; 42:1187-1207. [PMID: 34273915 DOI: 10.1002/humu.24261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/16/2021] [Accepted: 07/13/2021] [Indexed: 11/11/2022]
Abstract
Neurofibromatosis type 1 (NF1), type 2 (NF2), and schwannomatosis are a group of autosomal dominant disorders that predispose to the development of nerve sheath tumors. Pathogenic variants (PVs) that cause NF1 and NF2 are located in the NF1 and NF2 loci, respectively. To date, most variants associated with schwannomatosis have been identified in the SMARCB1 and LZTR1 genes, and a missense variant in the DGCR8 gene was recently reported to predispose to schwannomas. In spite of the high detection rate for PVs in NF1 and NF2 (over 90% of non-mosaic germline variants can be identified by routine genetic screening) underlying PVs for a proportion of clinical cases remain undetected. A higher proportion of non-NF2 schwannomatosis cases have no detected PV, with PVs currently only identified in around 70%-86% of familial cases and 30%-40% of non-NF2 sporadic schwannomatosis cases. A number of variants of uncertain significance have been observed for each disorder, many of them located in noncoding, regulatory, or intergenic regions. Here we summarize noncoding variants in this group of genes and discuss their established or potential role in the pathogenesis of NF1, NF2, and schwannomatosis.
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Affiliation(s)
- Cristina Perez-Becerril
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
| | - D Gareth Evans
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Miriam J Smith
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
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19
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N Abdel-Aziz N, Y El-Kamah G, A Khairat R, R Mohamed H, Z Gad Y, El-Ghor AM, Amr KS. Mutational spectrum of NF1 gene in 24 unrelated Egyptian families with neurofibromatosis type 1. Mol Genet Genomic Med 2021; 9:e1631. [PMID: 34080803 PMCID: PMC8683698 DOI: 10.1002/mgg3.1631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/19/2020] [Accepted: 02/09/2021] [Indexed: 11/25/2022] Open
Abstract
Background Neurofibromatosis 1 (NF1; OMIM# 162200) is a common autosomal dominant genetic disease [incidence: ~1:3500]. In 95% of cases, clinical diagnosis of the disease is based on the presence of at least two of the seven National Institute of Health diagnostic criteria. The molecular pathology underlying this disorder entails mutation in the NF1 gene. The aim of this study was to investigate clinical and molecular characteristics of a cohort of Egyptian NF1 patients. Method This study included 35 clinically diagnosed NF1 patients descending from 25 unrelated families. Patients had ≥2 NIH diagnostic criteria. Examination of NF1 gene was done through direct cDNA sequencing of multiple overlapping fragments. This was supplemented by NF1 multiple ligation dependent probe amplification (MLPA) analysis of leucocytic DNA. Results The clinical presentations encompassed, café‐au‐lait spots in 100% of probands, freckling (52%), neurofibromas (20%), Lisch nodules of the iris (12%), optic pathway glioma (8%), typical skeletal disorders (20%), and positive family history (32%). Mutations could be detected in 24 families (96%). Eight mutations (33%) were novel. Conclusion This study illustrates the underlying molecular pathology among Egyptian NF1 patients for the first time. It also reports on 8 novel mutation expanding pathogenic mutational spectra in the NF1 gene.
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Affiliation(s)
- Nahla N Abdel-Aziz
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Ghada Y El-Kamah
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Rabab A Khairat
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Hanan R Mohamed
- Zoology Department, Faculty of Science, Cairo University, Cairo, Egypt
| | - Yehia Z Gad
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Akmal M El-Ghor
- Zoology Department, Faculty of Science, Cairo University, Cairo, Egypt
| | - Khalda S Amr
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
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20
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Morbidoni V, Baschiera E, Forzan M, Fumini V, Ali DS, Giorgi G, Buson L, Desbats MA, Cassina M, Clementi M, Salviati L, Trevisson E. Hybrid Minigene Assay: An Efficient Tool to Characterize mRNA Splicing Profiles of NF1 Variants. Cancers (Basel) 2021; 13:cancers13050999. [PMID: 33673681 PMCID: PMC7957615 DOI: 10.3390/cancers13050999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/08/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is caused by heterozygous loss of function mutations in the NF1 gene. Although patients are diagnosed according to clinical criteria and few genotype-phenotype correlations are known, molecular analysis remains important. NF1 displays allelic heterogeneity, with a high proportion of variants affecting splicing, including deep intronic alleles and changes outside the canonical splice sites, making validation problematic. Next Generation Sequencing (NGS) technologies integrated with multiplex ligation-dependent probe amplification (MLPA) have largely overcome RNA-based techniques but do not detect splicing defects. A rapid minigene-based system was set up to test the effects of NF1 variants on splicing. We investigated 29 intronic and exonic NF1 variants identified in patients during the diagnostic process. The minigene assay showed the coexistence of multiple mechanisms of splicing alterations for seven variants. A leaky effect on splicing was documented in one de novo substitution detected in a sporadic patient with a specific phenotype without neurofibromas. Our splicing assay proved to be a reliable and fast method to validate novel NF1 variants potentially affecting splicing and to detect hypomorphic effects that might have phenotypic consequences, avoiding the requirement of patient's RNA.
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Affiliation(s)
- Valeria Morbidoni
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Elisa Baschiera
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Monica Forzan
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Valentina Fumini
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Dario Seif Ali
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Gianpietro Giorgi
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Lisa Buson
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Maria Andrea Desbats
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Matteo Cassina
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Maurizio Clementi
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Eva Trevisson
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
- Correspondence: ; Tel.: + 39-(04)-9821-1402
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21
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Ozarslan B, Russo T, Argenziano G, Santoro C, Piccolo V. Cutaneous Findings in Neurofibromatosis Type 1. Cancers (Basel) 2021; 13:463. [PMID: 33530415 PMCID: PMC7865571 DOI: 10.3390/cancers13030463] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/02/2021] [Accepted: 01/14/2021] [Indexed: 12/15/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a complex autosomal dominant disorder associated with germline mutations in the NF1 tumor suppressor gene. NF1 belongs to a class of congenital anomaly syndromes called RASopathies, a group of rare genetic conditions caused by mutations in the Ras/mitogen-activated protein kinase pathway. Generally, NF1 patients present with dermatologic manifestations. In this review the main features of café-au-lait macules, freckling, neurofibromas, juvenile xanthogranuloma, nevus anemicus and other cutaneous findings will be discussed.
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Affiliation(s)
| | - Teresa Russo
- Dermatology Unit, University of Campania Luigi Vanvitelli, 80100 Naples, Italy; (T.R.); (G.A.)
| | - Giuseppe Argenziano
- Dermatology Unit, University of Campania Luigi Vanvitelli, 80100 Naples, Italy; (T.R.); (G.A.)
| | - Claudia Santoro
- Department of Woman, Neurofibromatosis Referral Centre, Child and of General and Specialised Surgery, University of Campania Luigi Vanvitelli, 80100 Naples, Italy;
| | - Vincenzo Piccolo
- Dermatology Unit, University of Campania Luigi Vanvitelli, 80100 Naples, Italy; (T.R.); (G.A.)
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22
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Strowd RE, Plotkin SR. Familial Nervous System Tumor Syndromes. ACTA ACUST UNITED AC 2020; 26:1523-1552. [PMID: 33273171 DOI: 10.1212/con.0000000000000950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
PURPOSE OF REVIEW Although sporadic primary neoplasms account for the majority of nervous system tumors, familial nervous system tumor syndromes are important and clinically relevant conditions for the neurologist to understand. This article reviews common inherited nervous system tumor syndromes including neurofibromatosis type 1, neurofibromatosis type 2, schwannomatosis, tuberous sclerosis complex, and von Hippel-Lindau syndrome. The epidemiology, genetics, approach to diagnosis, neurologic and nonneurologic manifestations, and management options are reviewed. RECENT FINDINGS Awareness of the more common and clinically relevant familial nervous system tumor syndromes is important. These conditions teach us about the underlying biology that drives tumor development in the central and peripheral nervous systems including peripheral nerve sheath tumors (eg, neurofibroma, schwannoma), meningioma, vestibular schwannoma, subependymal giant cell astrocytoma, and hemangioblastoma. Knowledge of the clinical manifestations ensures that the neurologist will be able to diagnose these conditions, recommend appropriate surveillance, refer to specialists, and support optimal management. Important discoveries in the role of the underlying genetics have contributed to the launch of several novel drug trials for these tumors, which are changing therapeutic options for patients. SUMMARY Familial nervous system tumor syndromes are uncommon conditions that require specialized surveillance and management strategies. Coordination across a multidisciplinary team that includes neurologists, neuro-oncologists, radiologists, neurosurgeons, radiation oncologists, otolaryngologists, pathologists, neuropsychologists, physical medicine and rehabilitation specialists, and geneticists is necessary for the optimal treatment of these patients.
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23
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Physicians' adherence to published guidelines regarding the outpatient care of pediatric patients with neurofibromatosis type 1. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Neurofibromatosis type 1: New developments in genetics and treatment. J Am Acad Dermatol 2020; 84:1667-1676. [PMID: 32771543 DOI: 10.1016/j.jaad.2020.07.105] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022]
Abstract
Neurofibromatosis type 1 is the most common neurocutaneous syndrome, with a frequency of 1 in 2500 persons. Diagnosis is paramount in the pretumor stage to provide proper anticipatory guidance for a number of neoplasms, both benign and malignant. Loss-of-function mutations in the NF1 gene result in truncated and nonfunctional production of neurofibromin, a tumor suppressor protein involved in downregulating the RAS signaling pathway. New therapeutic and preventive options include tyrosine kinase inhibitors, mTOR inhibitors, interferons, and radiofrequency therapy. This review summarizes recent updates in genetics, mutation analysis assays, and treatment options targeting aberrant genetic pathways. We also propose modified diagnostic criteria and provide an algorithm for surveillance of patients with neurofibromatosis type 1.
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25
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Lee YH, Kwon MJ, Park JH, Jeong SJ, Kim TH, Jeong HW, Lee SH. Neurofibromatosis Type 1 with the Development of Pheochromocytoma and Breast Cancer. Intern Med 2020; 59:1665-1669. [PMID: 32269189 PMCID: PMC7402965 DOI: 10.2169/internalmedicine.4148-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/26/2020] [Indexed: 11/23/2022] Open
Abstract
A 40-year-old woman presented with a left adrenal incidentaloma. Based on the presence of café-au-lait spots, cutaneous neurofibroma, and family history, she was diagnosed with neurofibromatosis type 1 (NF1). Adrenal incidentaloma screening showed an elevated normetanephrine level; the left adrenal mass showed the uptake of I-123 meta-iodobenzylguanidine. She underwent left adrenalectomy, and pheochromocytoma was diagnosed. One year later, the results of a biopsy of a palpable mass in the left breast suggested invasive ductal carcinoma. The patient underwent neoadjuvant chemotherapy followed by left breast-conserving surgery. We herein report a rare case of an NF1 patient who developed both pheochromocytoma and breast cancer.
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Affiliation(s)
- Yu Hee Lee
- Department of Internal Medicine, College of Medicine, Inje University, Korea
| | - Min Jeong Kwon
- Department of Internal Medicine, College of Medicine, Inje University, Korea
| | - Jeong Hyun Park
- Department of Internal Medicine, College of Medicine, Inje University, Korea
| | - Su Jin Jeong
- Department of Pathology, College of Medicine, Inje University, Korea
| | - Tae Hyun Kim
- Department of Surgery, College of Medicine, Inje University, Korea
| | - Hae Woong Jeong
- Department of Radiology, College of Medicine, Inje University, Korea
| | - Soon Hee Lee
- Department of Internal Medicine, College of Medicine, Inje University, Korea
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26
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Lee H, Nelson SF. The frontiers of sequencing in undiagnosed neurodevelopmental diseases. Curr Opin Genet Dev 2020; 65:76-83. [PMID: 32599523 DOI: 10.1016/j.gde.2020.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/07/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022]
Abstract
Characterized by impairments in brain and central nervous system development, neurodevelopmental diseases causes are highly heterogeneous. Although many of these diseases are individually rare, collectively more than 3% of the children are reported to be affected with a type of neurodevelopmental diseases worldwide, and many remain undiagnosed even with current genomic tools. Identifying the genetic causes of these diseases allows better clinical management and expands our understanding of human neurodevelopment. Over the past decade, expansion of genomic sequencing and some methodologic improvements have improved molecular diagnostic yield as well as the discovery of novel genetic causes for wide spectrum of neurodevelopmental diseases. Here we review the current diagnostic workflow and propose ways of improving the diagnostic yield.
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Affiliation(s)
- Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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27
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Bianchessi D, Ibba MC, Saletti V, Blasa S, Langella T, Paterra R, Cagnoli GA, Melloni G, Scuvera G, Natacci F, Cesaretti C, Finocchiaro G, Eoli M. Simultaneous Detection of NF1, SPRED1, LZTR1, and NF2 Gene Mutations by Targeted NGS in an Italian Cohort of Suspected NF1 Patients. Genes (Basel) 2020; 11:genes11060671. [PMID: 32575496 PMCID: PMC7349720 DOI: 10.3390/genes11060671] [Citation(s) in RCA: 2] [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: 05/23/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/30/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) displays overlapping phenotypes with other neurocutaneous diseases such as Legius Syndrome. Here, we present results obtained using a next generation sequencing (NGS) panel including NF1, NF2, SPRED1, SMARCB1, and LZTR1 genes on Ion Torrent. Together with NGS, the Multiplex Ligation-Dependent Probe Amplification Analysis (MLPA) method was performed to rule out large deletions/duplications in NF1 gene; we validated the MLPA/NGS approach using Sanger sequencing on DNA or RNA of both positive and negative samples. In our cohort, a pathogenic variant was found in 175 patients; the pathogenic variant was observed in NF1 gene in 168 cases. A SPRED1 pathogenic variant was also found in one child and in a one year old boy, both NF2 and LZTR1 pathogenic variants were observed; in addition, we identified five LZTR1 pathogenic variants in three children and two adults. Six NF1 pathogenic variants, that the NGS analysis failed to identify, were detected on RNA by Sanger. NGS allows the identification of novel mutations in five genes in the same sequencing run, permitting unambiguous recognition of disorders with overlapping phenotypes with NF1 and facilitating genetic counseling and a personalized follow-up.
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Affiliation(s)
- Donatella Bianchessi
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Maria Cristina Ibba
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (V.S.); (G.M.)
| | - Stefania Blasa
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza dell’Ateneo Nuovo, 1, 20126 Milan, Italy
| | - Tiziana Langella
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian, 20133 Milan, Italy
| | - Rosina Paterra
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Giulia Anna Cagnoli
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (G.A.C.); (F.N.); (C.C.)
| | - Giulia Melloni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (V.S.); (G.M.)
| | - Giulietta Scuvera
- Pediatric Highly Intensive Care Unit, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy;
| | - Federica Natacci
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (G.A.C.); (F.N.); (C.C.)
| | - Claudia Cesaretti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (G.A.C.); (F.N.); (C.C.)
| | - Gaetano Finocchiaro
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Marica Eoli
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
- Correspondence:
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28
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Whiffin N, Karczewski KJ, Zhang X, Chothani S, Smith MJ, Evans DG, Roberts AM, Quaife NM, Schafer S, Rackham O, Alföldi J, O'Donnell-Luria AH, Francioli LC, Cook SA, Barton PJR, MacArthur DG, Ware JS. Characterising the loss-of-function impact of 5' untranslated region variants in 15,708 individuals. Nat Commun 2020; 11:2523. [PMID: 32461616 PMCID: PMC7253449 DOI: 10.1038/s41467-019-10717-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/23/2019] [Indexed: 01/17/2023] Open
Abstract
Upstream open reading frames (uORFs) are tissue-specific cis-regulators of protein translation. Isolated reports have shown that variants that create or disrupt uORFs can cause disease. Here, in a systematic genome-wide study using 15,708 whole genome sequences, we show that variants that create new upstream start codons, and variants disrupting stop sites of existing uORFs, are under strong negative selection. This selection signal is significantly stronger for variants arising upstream of genes intolerant to loss-of-function variants. Furthermore, variants creating uORFs that overlap the coding sequence show signals of selection equivalent to coding missense variants. Finally, we identify specific genes where modification of uORFs likely represents an important disease mechanism, and report a novel uORF frameshift variant upstream of NF2 in neurofibromatosis. Our results highlight uORF-perturbing variants as an under-recognised functional class that contribute to penetrant human disease, and demonstrate the power of large-scale population sequencing data in studying non-coding variant classes.
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Affiliation(s)
- Nicola Whiffin
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK.
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
| | - Konrad J Karczewski
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Xiaolei Zhang
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
| | - Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Miriam J Smith
- NW Genomic Laboratory Hub, Centre for Genomic Medicine, Division of Evolution and Genomic Science, St Mary's Hospital, University of Manchester, Oxford Road, Manchester, M13 9WL, UK
| | - D Gareth Evans
- NW Genomic Laboratory Hub, Centre for Genomic Medicine, Division of Evolution and Genomic Science, St Mary's Hospital, University of Manchester, Oxford Road, Manchester, M13 9WL, UK
| | - Angharad M Roberts
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
| | - Nicholas M Quaife
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- National Heart Centre Singapore, 5 Hospital Drive, Singapore, 169609, Singapore
| | - Owen Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Jessica Alföldi
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Anne H O'Donnell-Luria
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Laurent C Francioli
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Stuart A Cook
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- National Heart Centre Singapore, 5 Hospital Drive, Singapore, 169609, Singapore
| | - Paul J R Barton
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
| | - Daniel G MacArthur
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
- NIHR Royal Brompton Cardiovascular Research Centre, Royal Brompton and Harefield National Health Service Foundation Trust, Sydney Street, London, SW3 6NP, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
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Abstract
Phakomatoses present with characteristic findings on the skin, central or peripheral nervous system, and tumors. Neurofibromatosis type 1 is the most common syndrome and is characterized by Café-au-lait macules, intertriginous freckling, Lisch nodules, and tumors including neurofibromas, malignant peripheral nerve sheath tumors, and gliomas. Tuberous Sclerosis Complex is characterized by benign hamartomas presenting with hypomelanotic macules, shagreen patches, angiofibromas, confetti lesions and tumors including cortical tubers, subependymal nodules, subependymal giant cell astrocytomas and tumors of the kidney, lung, and heart. Managing these disorders requires disease specific supportive care, tumor monitoring, surveillance for selected cancers, and treatment of comorbid conditions.
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Affiliation(s)
- Benjamin Becker
- Department of Neurology, Wake Forest Baptist Health, 1 Medical Center Boulevard, Winston Salem, NC 27157, USA.
| | - Roy E Strowd
- Department of Neurology, Wake Forest Baptist Health, 1 Medical Center Boulevard, Winston Salem, NC 27157, USA; Department of Internal Medicine, Section on Hematology and Oncology, Wake Forest Baptist Health, Winston Salem, NC 27157, USA; Translational Science Institute, Wake Forest Baptist Health, Winston Salem, NC 27157, USA
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Bergqvist C, Servy A, Valeyrie-Allanore L, Ferkal S, Combemale P, Wolkenstein P. Neurofibromatosis 1 French national guidelines based on an extensive literature review since 1966. Orphanet J Rare Dis 2020; 15:37. [PMID: 32014052 PMCID: PMC6998847 DOI: 10.1186/s13023-020-1310-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/17/2020] [Indexed: 12/13/2022] Open
Abstract
Neurofibromatosis type 1 is a relatively common genetic disease, with a prevalence ranging between 1/3000 and 1/6000 people worldwide. The disease affects multiple systems with cutaneous, neurologic, and orthopedic as major manifestations which lead to significant morbidity or mortality. Indeed, NF1 patients are at an increased risk of malignancy and have a life expectancy about 10-15 years shorter than the general population. The mainstay of management of NF1 is a patient-centered longitudinal care with age-specific monitoring of clinical manifestations, aiming at the early recognition and symptomatic treatment of complications as they occur. Protocole national de diagnostic et de soins (PNDS) are mandatory French clinical practice guidelines for rare diseases required by the French national plan for rare diseases. Their purpose is to provide health care professionals with guidance regarding the optimal diagnostic and therapeutic management of patients affected with a rare disease; and thus, harmonizing their management nationwide. PNDS are usually developed through a critical literature review and a multidisciplinary expert consensus. The purpose of this article is to present the French guidelines on NF1, making them even more available to the international medical community. We further dwelled on the emerging new evidence that might have therapeutic potential or a strong impact on NF1 management in the coming feature. Given the complexity of the disease, the management of children and adults with NF1 entails the full complement healthcare providers and communication among the various specialties.
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Affiliation(s)
- Christina Bergqvist
- Faculty of medicine, Université Paris-Est Creteil (UPEC), F-94010 Créteil Cedex, France
- Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, Service de Dermatologie, F-94010 Créteil, France
| | - Amandine Servy
- Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, Service de Dermatologie, F-94010 Créteil, France
| | - Laurence Valeyrie-Allanore
- INSERM, Centre d’Investigation Clinique 006, Referral Center of Neurofibromatosis, Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, F-94010 Créteil, France
| | - Salah Ferkal
- INSERM, Centre d’Investigation Clinique 006, Referral Center of Neurofibromatosis, Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, F-94010 Créteil, France
| | - Patrick Combemale
- Rhône-Alpes Auvergne Competence Center for the treatment of Neurofibromatosis type 1, Léon Bérard Comprehensive Cancer Center, Hôpitaux Universitaires de Lyon, Université de Lyon, F-69008 Lyon, France
| | - Pierre Wolkenstein
- Faculty of medicine, Université Paris-Est Creteil (UPEC), F-94010 Créteil Cedex, France
- Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, Service de Dermatologie, F-94010 Créteil, France
- INSERM, Centre d’Investigation Clinique 006, Referral Center of Neurofibromatosis, Assistance Publique-Hôpital Paris (AP-HP), Hôpital Henri-Mondor, F-94010 Créteil, France
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31
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Yao R, Yu T, Xu Y, Yu L, Wang J, Wang X, Wang J, Shen Y. Clinical Presentation and Novel Pathogenic Variants among 68 Chinese Neurofibromatosis 1 Children. Genes (Basel) 2019; 10:genes10110847. [PMID: 31717729 PMCID: PMC6896037 DOI: 10.3390/genes10110847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/08/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Neurofibromatosis 1 (NF1) is one of the most common dominantly inherited genetic disorders worldwide, with an age-dependent phenotypic expression. Exploring the mutational spectrum and clinical presentation of NF1 patients at different ages from a diverse population will aid the understanding of genotype–phenotype correlations. Methods: In this study, 95 Chinese children with clinical suspicion of NF1 mainly due to the presence of multiple café-au-lait macules (CALMs) were subjected to medical exome-sequencing analysis and Sanger confirmation of pathogenic variants. Clinical presentations were evaluated regarding dermatological, ocular, neurological, and behavioral features. Results: Pathogenic or likely pathogenic NF1 variants were detected in 71.6% (68/95) of patients; 20 pathogenic variants were not previously reported, indicating that Chinese NF1 patients are still understudied. Parental Sanger sequencing confirmation revealed 77.9% of de novo variants, a percentage that was much higher than expected. The presence of a higher number of NF1-related features at young ages was correlated with positive diagnostic findings. In addition to CALMs, neurological and behavioral features had a high expression among Chinese NF1 children. We attempted to correlate short stature with the locations of the pathogenic variants across the NF1 gene. It is interesting to notice that variants detected in the C-terminal region of the NF1 gene were less likely to be associated with short stature among the NF1 patients, whereas variants at the N-terminal were highly penetrant for the short stature phenotype. Conclusion: Novel NF1 pathogenic variants are yet to be uncovered in under-studied NF1 patient populations; their identification will help to reveal novel genotype–phenotype correlations.
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Affiliation(s)
- Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center—Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; (R.Y.); (T.Y.); (Y.X.); (L.Y.); (J.W.)
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center—Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; (R.Y.); (T.Y.); (Y.X.); (L.Y.); (J.W.)
| | - Yufei Xu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center—Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; (R.Y.); (T.Y.); (Y.X.); (L.Y.); (J.W.)
| | - Li Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center—Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; (R.Y.); (T.Y.); (Y.X.); (L.Y.); (J.W.)
| | - Jiwen Wang
- Department of Pediatrics, Shanghai Children’s Medical Center—Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; (J.W.); (X.W.)
| | - Xiumin Wang
- Department of Pediatrics, Shanghai Children’s Medical Center—Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; (J.W.); (X.W.)
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center—Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; (R.Y.); (T.Y.); (Y.X.); (L.Y.); (J.W.)
| | - Yiping Shen
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center—Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; (R.Y.); (T.Y.); (Y.X.); (L.Y.); (J.W.)
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
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32
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Waqar M, Huson S, Evans DG, Ealing J, Karabatsou K, George KJ, Soh C. C2 neurofibromas in neurofibromatosis type 1: genetic and imaging characteristics. J Neurosurg Spine 2019; 30:126-132. [PMID: 30485203 DOI: 10.3171/2018.7.spine171340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 07/10/2018] [Indexed: 12/31/2022]
Abstract
OBJECTIVEC2 nerve root neurofibromas have been reported frequently in patients with neurofibromatosis type 1 (NF1), although their genetic and imaging characteristics are unexplored. The aim of this study was to characterize genetic and spinal imaging findings in a large cohort of NF1 patients with C2 neurofibromas.METHODSThe authors performed a review of national NF1 referrals between 2009 and 2016. Inclusion criteria were at least 1 C2 root neurofibroma and cervical-spine or whole-spine MRI scans available for analysis. Blinded imaging review was performed by a neuroradiologist with an interest in NF1.RESULTSFifty-four patients with 106 C2 neurofibromas were included. The median age was 32.5 years (range 15-61 years), and there were slightly more male patients (33 vs 21 female patients). Splice-site (30%) and missense (20%) variants were frequent. Spinal neurofibromas were distributed in all spine regions (65%) or in the cervical spine alone (22%). Most (93%) C2 neurofibromas were visible on MRI scans of the head. Intradural invasion and cord compression in the cervical spine included the C2 level in 95% and 80% of patients, respectively. Compared with all other cervical spine neurofibromas in these patients, C2 neurofibromas had higher rates of intraspinal extension (75% vs 32%; OR 6.20, 95% CI 3.85-9.97; p < 0.001), intradural invasion (53% vs 26%; OR 3.20, 95% CI 2.08-4.92; p < 0.001), and cord compression (25% vs 13%; OR 2.26, 95% CI 1.35-3.79; p = 0.002). However, C2 neurofibromas had lower rates of extraforaminal growth beyond the transverse process (12% vs 62%; OR 0.09, 95% CI 0.05-0.16; p < 0.001).CONCLUSIONSC2 neurofibromas are associated with an aggressive intraspinal phenotype, limited growth outside the spinal canal, and an uncommon genetic profile. These observations require future study.
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Affiliation(s)
- Mueez Waqar
- Departments of1Neurosurgery.,2Manchester Academic Health Sciences Centre, Division of Evolution and Genomic Sciences, The University of Manchester, United Kingdom
| | - Susan Huson
- 2Manchester Academic Health Sciences Centre, Division of Evolution and Genomic Sciences, The University of Manchester, United Kingdom.,3Department of Neurogenetics, Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester; and
| | - D Gareth Evans
- 2Manchester Academic Health Sciences Centre, Division of Evolution and Genomic Sciences, The University of Manchester, United Kingdom.,3Department of Neurogenetics, Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester; and
| | - John Ealing
- 2Manchester Academic Health Sciences Centre, Division of Evolution and Genomic Sciences, The University of Manchester, United Kingdom.,4Neurogenetics, and
| | - Konstantina Karabatsou
- Departments of1Neurosurgery.,2Manchester Academic Health Sciences Centre, Division of Evolution and Genomic Sciences, The University of Manchester, United Kingdom
| | - K Joshi George
- Departments of1Neurosurgery.,2Manchester Academic Health Sciences Centre, Division of Evolution and Genomic Sciences, The University of Manchester, United Kingdom
| | - Calvin Soh
- 2Manchester Academic Health Sciences Centre, Division of Evolution and Genomic Sciences, The University of Manchester, United Kingdom.,5Neuroradiology, Salford Royal NHS Foundation Trust, Salford
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33
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Zhu G, Zheng Y, Liu Y, Yan A, Hu Z, Yang Y, Xiang S, Li L, Chen W, Peng Y, Zhong N, Mei H. Identification and characterization of NF1 and non-NF1 congenital pseudarthrosis of the tibia based on germline NF1 variants: genetic and clinical analysis of 75 patients. Orphanet J Rare Dis 2019; 14:221. [PMID: 31533797 PMCID: PMC6751843 DOI: 10.1186/s13023-019-1196-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/04/2019] [Indexed: 12/13/2022] Open
Abstract
Background Congenital pseudarthrosis of the tibia (CPT) is a rare disease. Some patients present neurofibromatosis type 1 (NF1), while some others do not manifest NF1 (non-NF1). The etiology of CPT, particularly non-NF1 CPT, is not well understood. Here we screened germline variants of 75 CPT cases, including 55 NF1 and 20 non-NF1. Clinical data were classified and analyzed based on NF1 gene variations to investigate the genotype-phenotype relations of the two types of patients. Results Using whole-exome sequencing and Multiplex Ligation-Dependent Probe Amplification, 44 out of 55 NF1 CPT patients (80.0%) were identified as carrying pathogenic variants of the NF1 gene. Twenty-five variants were novel; 53.5% of variants were de novo, and a higher proportion of their carriers presented bone fractures compared to inherited variant carriers. No NF1 pathogenic variants were found in all 20 non-NF1 patients. Clinical features comparing NF1 CPT to non-NF1 CPT did not show significant differences in bowing or fracture onset, lateralization, tissue pathogenical results, abnormality of the proximal tibial epiphysis, and follow-up tibial union after surgery. A considerably higher proportion of non-NF1 patients have cystic lesion (Crawford type III) and used braces after surgery. Conclusions We analyzed a large cohort of non-NF1 and NF1 CPT patients and provided a new perspective for genotype-phenotype features related to germline NF1 variants. Non-NF1 CPT in general had similar clinical features of the tibia as NF1 CPT. Germline NF1 pathogenic variants could differentiate NF1 from non-NF1 CPT but could not explain the CPT heterogeneity of NF1 patients. Our results suggested that non-NF1 CPT was probably not caused by germline NF1 pathogenic variants. In addition to NF1, other genetic variants could also contribute to CPT pathogenesis. Our findings would facilitate the interpretation of NF1 pathogenic variants in CPT genetic counseling. Supplementary information The online version of this article (10.1186/s13023-019-1196-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guanghui Zhu
- Department of Pediatric Orthopaedics, Hunan Children's Hospital, The Pediatric Academy of the University of South China, 86# Ziyuan Road, Changsha, Hunan Province, 410007, People's Republic of China
| | - Yu Zheng
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan Province, People's Republic of China.,Center for Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan Province, People's Republic of China
| | - Yaoxi Liu
- Department of Pediatric Orthopaedics, Hunan Children's Hospital, The Pediatric Academy of the University of South China, 86# Ziyuan Road, Changsha, Hunan Province, 410007, People's Republic of China
| | - An Yan
- Department of Pediatric Orthopaedics, Hunan Children's Hospital, The Pediatric Academy of the University of South China, 86# Ziyuan Road, Changsha, Hunan Province, 410007, People's Republic of China
| | - Zhengmao Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, Hunan Province, People's Republic of China
| | - Yongjia Yang
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan Province, People's Republic of China
| | - Shiting Xiang
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan Province, People's Republic of China
| | - Liping Li
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan Province, People's Republic of China
| | - Weijian Chen
- Pathology Department, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan Province, People's Republic of China
| | - Yu Peng
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan Province, People's Republic of China
| | - Nanbert Zhong
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan Province, People's Republic of China. .,New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA.
| | - Haibo Mei
- Department of Pediatric Orthopaedics, Hunan Children's Hospital, The Pediatric Academy of the University of South China, 86# Ziyuan Road, Changsha, Hunan Province, 410007, People's Republic of China.
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Breast cancer in neurofibromatosis 1: survival and risk of contralateral breast cancer in a five country cohort study. Genet Med 2019; 22:398-406. [PMID: 31495828 PMCID: PMC7000349 DOI: 10.1038/s41436-019-0651-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/27/2019] [Indexed: 11/23/2022] Open
Abstract
Purpose Neurofibromatosis 1 (NF1) is an autosomal dominant condition caused
by pathogenic variants of the NF1 gene. A
markedly increased risk of breast cancer is associated with NF1. We have
determined the breast cancer survival and risk of contralateral breast cancer in
NF1. Methods We included 142 women with NF1 and breast cancer from five cohorts
in Europe and 335 women without NF1 screened for other familial breast cancers.
Risk of contralateral breast cancer and death were assessed by Kaplan–Meier
analysis with delayed entry. Results One hundred forty-two women with NF1 were diagnosed for breast
cancer at a median age of 46.9 years (range 27.0–84.3 years) and then followed
up for 1235 person-years (mean = 8.70 years). Twelve women had contralateral
breast cancer with a rate of 10.5 per 1000 years. Cumulative risk for
contralateral breast cancer was 26.5% in 20 years. Five and 10-year all-cause
survival was 64.9% (95% confidence interval [CI] = 54.8–76.8) and 49.8%
(95%CI = 39.3–63.0). Breast cancer–specific 10-year survival was 64.2% (95%
CI = 53.5–77.0%) compared with 91.2% (95% CI = 87.3–95.2%) in the non-NF1
age-matched population at increased risk of breast cancer. Conclusion Women with NF1 have a substantial contralateral breast cancer
incidence and poor survival. Early start of breast cancer screening may be a way
to improve the survival.
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35
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Setrajcic Dragos V, Blatnik A, Klancar G, Stegel V, Krajc M, Blatnik O, Novakovic S. Two Novel NF1 Pathogenic Variants Causing the Creation of a New Splice Site in Patients With Neurofibromatosis Type I. Front Genet 2019; 10:762. [PMID: 31507634 PMCID: PMC6714493 DOI: 10.3389/fgene.2019.00762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/17/2019] [Indexed: 01/12/2023] Open
Abstract
Neurofibromatosis type I (NF1) is one of the most common autosomal dominant disorders, since the estimated incidence is one in 3,500 births. In this study, we present bioinformatical and functional characterization of two novel splicing NF1 variants, detected in NF1 patients. Patient 1, carrying NF1:c.122A>T, which introduces a new exonic 5’ donor splice site, was diagnosed with hormone-positive, Her-2-negative breast cancer at the age of 47. She had an atypical presentation of NF1, with few café-au-lait spots and no Lisch nodules. Patient developed a hemothorax due to subclavian artery rupture, which has previously been described as an extremely rare complication of NF1. Patient 2, carrying NF1:c.7395-17T>G that creates a new intronic 3’ acceptor splice site, had quite a typical clinical presentation of NF1: formations on her tongue in the region of her left metacarpal bones and on her left foot, plexiform neurofibroma in her pelvis, several café-au-lait spots, and axillary freckling. She was also diagnosed with cognitive impairment. In the report, we are presenting two novel variants which were successfully classified based on NGS and mRNA analysis. Based on results of mRNA analysis, both variants were classified as likely pathogenic according to ACMG guidelines applying evidence categories PS3, PM2, PP3, and PP1 supporting. By characterizing those two novel NF1 splicing variants, we have confirmed the neurofibromatosis type I phenotype in the two probands.
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Affiliation(s)
- Vita Setrajcic Dragos
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Ana Blatnik
- Cancer Genetics Clinic, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Gasper Klancar
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Vida Stegel
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Mateja Krajc
- Cancer Genetics Clinic, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Olga Blatnik
- Department of Pathology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Srdjan Novakovic
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
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Al-Sharefi A, Javaid U, Perros P, Ealing J, Truran P, Nag S, Kamaruddin S, Abouglila K, Cains F, Lewis L, James RA. Clinical Presentation and Outcomes of Phaeochromocytomas/Paragangliomas in Neurofibromatosis Type 1. EUROPEAN ENDOCRINOLOGY 2019; 15:95-100. [PMID: 31616500 PMCID: PMC6785954 DOI: 10.17925/ee.2019.15.2.95] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 04/25/2019] [Indexed: 12/23/2022]
Abstract
Introduction: Patients with neurofibromatosis type 1 (NF1) are at risk of developing phaeochromocytomas/paragangliomas (PHAEO/PG). Unlike in other familial PHAEO/PG syndromes, there are no published guidelines regarding screening in asymptomatic or normotensive patients with NF1. This strategy may be associated with preventable morbidities in those patients who ultimately present with symptomatic PHAEO/PG. Objective: To describe the mode of presentation and the incidence of adverse clinical outcomes attributed to PHAEO/PG in NF1. Methods: A retrospective study was performed in a tertiary referral centre in collaboration with a national complex NF1 centre. Hospital records and databases between 1998–2018 were searched. Results: Twenty-seven patients with NF1 and PHAEO/PG were identified. In all but one, PHAEO/PG was diagnosed after NF1. The median age at the time of diagnosis of PHAEO/PG was 43 years (range 22–65) and 21/27 (78%) were females. The diagnosis was mostly incidental in 13/27 (48%) while classical PHAEO/PG symptoms were found in 15/27 (56%), and hypertension was found in 14/27 (52%) of NF1 patients prior to PHAEO/PG diagnosis. No patient had undergone biochemical screening for PHAEO/PG. Metastatic disease was evident in 2/27 patients, 8 suffered potentially avoidable complications attributed to PHAEO/PG (including two deaths). Conclusion: The course of PHAEO/PG in NF1 is associated with an unpredictable presentation and potentially avoidable adverse outcomes. We recommend that routine biochemical screening for PHAEO/PG should be part of the care package offered to all patients with NF1 by regular measurements of plasma free or urinary fractionated metanephrines starting from early adolescence and repeated every 3 years.
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Affiliation(s)
- Ahmed Al-Sharefi
- Department of Endocrinology, The Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon-Tyne, UK
| | - Usman Javaid
- Department of Endocrinology, The Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon-Tyne, UK
| | - Petros Perros
- Department of Endocrinology, The Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon-Tyne, UK
| | - John Ealing
- Manchester Centre for Clinical Neuroscience, Salford Royal NHS Foundation Trust, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Peter Truran
- Department of Endocrine Surgery, The Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Sath Nag
- Department of Endocrinology, The James Cook University Hospital, South Tees Hospitals NHS Foundation Trust, Middlesbrough, UK
| | - Shafie Kamaruddin
- Department of Endocrinology, County Durham and Darlington NHS Foundation Trust, Durham, UK
| | - Kamal Abouglila
- Department of Endocrinology, County Durham and Darlington NHS Foundation Trust, Durham, UK
| | - Fiona Cains
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Lauren Lewis
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Robert Andrew James
- Department of Endocrinology, The Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon-Tyne, UK
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Karwacki MW, Wysocki M, Perek-Polnik M, Jatczak-Gaca A. Coordinated medical care for children with neurofibromatosis type 1 and related RASopathies in Poland. Arch Med Sci 2019; 17:1221-1231. [PMID: 34522251 PMCID: PMC8425254 DOI: 10.5114/aoms.2019.85143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/12/2019] [Indexed: 11/17/2022] Open
Abstract
Coordinated medical care offered in Poland for patients suffering from neurofibromatosis type 1 and related RASopathies combines complex multispecialty consultation with permanent supervision and the patient's oriented longitudinal care. Neurofibromatosis type 1 is one of the most common single gene disorders in the global population, observed in 1 out of 2500-3000 live births. It is a primary neoplasia disease with 100% penetration of the gene mutation but remarkable age-dependent onset of different disease signs and symptoms, outstanding clinical heterogeneity between patients even in one family and lack of genotype-phenotype correlation, a high rate of spontaneous mutation exceeding 50%, and multiple comorbidities among which increased risk of malignancy is the most important. Medical practice proved that not only patient-oriented complex but also coordinated care provided in centers of competence is indispensable for patients and the families and provides a sense of medical security to them in conjunction with public health costs rationalization.
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Affiliation(s)
- Marek W. Karwacki
- Coordinated Care Center for Neurofibromatoses and related RASopathies, Department of Pediatrics, Hematology and Oncology, Medical University of Warsaw, Poland
| | - Mariusz Wysocki
- Department of Paediatrics, Haematology and Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Poland
| | - Marta Perek-Polnik
- Neuro-oncology Division, Department of Oncology, The Children’s Memorial Health Institute, Warsaw, Poland
| | - Agnieszka Jatczak-Gaca
- Department of Paediatrics, Haematology and Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Poland
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38
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D’Angelo F, Ceccarelli M, Tala, Garofano L, Zhang J, Frattini V, Caruso FP, Lewis G, Alfaro KD, Bauchet L, Berzero G, Cachia D, Cangiano M, Capelle L, de Groot J, DiMeco F, Ducray F, Farah W, Finocchiaro G, Goutagny S, Kamiya-Matsuoka C, Lavarino C, Loiseau H, Lorgis V, Marras CE, McCutcheon I, Nam DH, Ronchi S, Saletti V, Seizeur R, Slopis J, Suñol M, Vandenbos F, Varlet P, Vidaud D, Watts C, Tabar V, Reuss DE, Kim SK, Meyronet D, Mokhtari K, Salvador H, Bhat KP, Eoli M, Sanson M, Lasorella A, lavarone A. The molecular landscape of glioma in patients with Neurofibromatosis 1. Nat Med 2019; 25:176-187. [PMID: 30531922 PMCID: PMC6857804 DOI: 10.1038/s41591-018-0263-8] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/17/2018] [Indexed: 12/30/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a common tumor predisposition syndrome in which glioma is one of the prevalent tumors. Gliomagenesis in NF1 results in a heterogeneous spectrum of low- to high-grade neoplasms occurring during the entire lifespan of patients. The pattern of genetic and epigenetic alterations of glioma that develops in NF1 patients and the similarities with sporadic glioma remain unknown. Here, we present the molecular landscape of low- and high-grade gliomas in patients affected by NF1 (NF1-glioma). We found that the predisposing germline mutation of the NF1 gene was frequently converted to homozygosity and the somatic mutational load of NF1-glioma was influenced by age and grade. High-grade tumors harbored genetic alterations of TP53 and CDKN2A, frequent mutations of ATRX associated with Alternative Lengthening of Telomere, and were enriched in genetic alterations of transcription/chromatin regulation and PI3 kinase pathways. Low-grade tumors exhibited fewer mutations that were over-represented in genes of the MAP kinase pathway. Approximately 50% of low-grade NF1-gliomas displayed an immune signature, T lymphocyte infiltrates, and increased neo-antigen load. DNA methylation assigned NF1-glioma to LGm6, a poorly defined Isocitrate Dehydrogenase 1 wild-type subgroup enriched with ATRX mutations. Thus, the profiling of NF1-glioma defined a distinct landscape that recapitulates a subset of sporadic tumors.
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Affiliation(s)
- Fulvio D’Angelo
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA.,BIOGEM Istituto di Ricerche Genetiche ‘G. Salvatore’, Ariano Irpino, Italy.,These authors contributed equally: F. D’Angelo, M. Ceccarelli
| | - Michele Ceccarelli
- BIOGEM Istituto di Ricerche Genetiche ‘G. Salvatore’, Ariano Irpino, Italy.,Department of Science and Technology, Università degli Studi del Sannio, Benevento, Italy.,These authors contributed equally: F. D’Angelo, M. Ceccarelli
| | - Tala
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Luciano Garofano
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA.,BIOGEM Istituto di Ricerche Genetiche ‘G. Salvatore’, Ariano Irpino, Italy
| | - Jing Zhang
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Véronique Frattini
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Francesca P. Caruso
- BIOGEM Istituto di Ricerche Genetiche ‘G. Salvatore’, Ariano Irpino, Italy.,Department of Science and Technology, Università degli Studi del Sannio, Benevento, Italy
| | - Genevieve Lewis
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Kristin D. Alfaro
- The University of Texas M.D. Anderson Cancer Center John Mendelsohn Faculty Center (FC7.3025) – Neuro-Oncology – Unit 0431, Houston, TX, USA
| | - Luc Bauchet
- Department of Neurosurgery, Gui de Chauliac Hospital, Montpellier University Medical Center, Montpellier, France
| | - Giulia Berzero
- Sorbonne Universités UPMC Université Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, APHP, Paris, France
| | - David Cachia
- Department of Neuro-Oncology, Medical University of South Carolina, Charleston, SC, USA.,Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, USA
| | - Mario Cangiano
- BIOGEM Istituto di Ricerche Genetiche ‘G. Salvatore’, Ariano Irpino, Italy
| | - Laurent Capelle
- AP-HP, Hôpital de la Pitié-Salpêtrière, Service de Neurochirurgie, Paris, France
| | - John de Groot
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Francesco DiMeco
- Department of Neurological Surgery, Carlo Besta Neurological Institute, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Hunterian Brain Tumor Research Laboratory CRB2 2M41, Baltimore, MD, USA
| | - François Ducray
- Service de Neuro-Oncologie, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, Department of Cancer Cell Plasticity, Cancer Research Center of Lyon, INSERM U1052, CNRS UMR5286, Lyon, France
| | - Walid Farah
- Department of Neurosurgery, CHU, Dijon, France
| | - Gaetano Finocchiaro
- Unit of Molecular Neuro-Oncology, IRCCS Foundation, Carlo Besta Neurological Institute, Milan, Italy
| | - Stéphane Goutagny
- Service de Neurochirurgie, Hôpital Beaujon, Assistance PubliqueHôpitaux de Paris, Clichy, France
| | | | - Cinzia Lavarino
- Developmental Tumor Laboratory, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Hugues Loiseau
- Department of Neurosurgery, Bordeaux University Hospital. Labex TRAIL (ANR-10-LABX-57). EA 7435 – IMOTION Bordeaux University, Bordeaux, France
| | - Véronique Lorgis
- Department of Medical Oncology, Centre GF Leclerc, Dijon, France
| | - Carlo E. Marras
- Pediatric Neurosurgery Unit, Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children’s Hospital, Rome, Italy
| | - Ian McCutcheon
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Do-Hyun Nam
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Susanna Ronchi
- Sorbonne Universités UPMC Université Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, APHP, Paris, France
| | - Veronica Saletti
- Developmental Neurology Unit, IRCCS Foundation, Carlo Besta Neurological Institute, Milan, Italy
| | - Romuald Seizeur
- Service de Neurochirurgie, Hôpital de la Cavale Blanche, CHRU de Brest, Université de Brest, Brest, France
| | - John Slopis
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Fanny Vandenbos
- Central Laboratory of Pathology, Pasteur I University Hospital, Nice, France
| | - Pascale Varlet
- Department of Neuropathology, Sainte-Anne Hospital, Paris, France.,IMA-Brain, Inserm U894, Institute of Psychiatry and Neuroscience of Paris, Paris, France
| | - Dominique Vidaud
- EA7331, Université Paris Descartes, France; Service de Génétique et Biologie Moléculaires, Hôpital Cochin, AP-HP, Paris, France
| | - Colin Watts
- Institute of Cancer and Genomic Sciences University of Birmingham Edgbaston, Birmingham, United Kingdom
| | - Viviane Tabar
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David E. Reuss
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Seoul National University Children’s Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - David Meyronet
- Centre de Pathologie Et Neuropathologie Est Hospices Civils de Lyon, Lyon, France
| | - Karima Mokhtari
- Sorbonne Universités UPMC Université Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, APHP, Paris, France
| | - Hector Salvador
- Pediatric Oncology Unit, Hospital Sant Joan de Déu, Esplugues, Barcelona, Spain
| | - Krishna P. Bhat
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Marica Eoli
- Unit of Molecular Neuro-Oncology, IRCCS Foundation, Carlo Besta Neurological Institute, Milan, Italy
| | - Marc Sanson
- Sorbonne Universités UPMC Université Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, APHP, Paris, France
| | - Anna Lasorella
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA. .,Department of Pediatrics, Columbia University Medical Center, New York, NY, USA. .,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
| | - Antonio lavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.,Department of Neurology, Columbia University Medical Center, New York, NY, USA.,These authors jointly supervised this work: A. Lasorella, A. Iavarone.,Correspondence and requests for materials should be addressed to A.L. or A.I. ;
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Evans DG, Howell SJ, Peltonen J. Association Between Invasive Lobular Breast Cancer and Mutations in the Mismatch Repair Gene MSH6. JAMA Oncol 2019; 5:119-120. [PMID: 30629136 DOI: 10.1001/jamaoncol.2018.6905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom.,The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Sacha J Howell
- The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Juha Peltonen
- Department of Cell Biology and Anatomy, University of Turku, Turku, Finland
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40
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Gürsoy S, Erçal D. Genetic Evaluation of Common Neurocutaneous Syndromes. Pediatr Neurol 2018; 89:3-10. [PMID: 30424961 DOI: 10.1016/j.pediatrneurol.2018.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
The neurocutaneous syndromes are a group of multisystem disorders that affect the skin and central nervous system. Neurofibromatosis 1, neurofibromatosis 2, tuberous sclerosis complex, and Sturge-Weber syndrome are the four major neurocutaneous disorders that mainly present in childhood. In this review, we discuss the clinical findings and genetic diagnosis, related genes/pathways and genotype-phenotype correlations of these four neurocutaneous syndromes.
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Affiliation(s)
- Semra Gürsoy
- Department of Pediatric Genetics, Dr. Behcet Uz Children's Hospital, Izmir, Turkey.
| | - Derya Erçal
- Department of Pediatric Genetics, Dokuz Eylül University Medical School, Izmir, Turkey
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41
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Evans DG, Howell SJ, Frayling IM, Peltonen J. Gene panel testing for breast cancer should not be used to confirm syndromic gene associations. NPJ Genom Med 2018; 3:32. [PMID: 30510771 PMCID: PMC6255919 DOI: 10.1038/s41525-018-0071-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/02/2018] [Indexed: 12/24/2022] Open
Affiliation(s)
- D Gareth Evans
- 1Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL UK.,2Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,3The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX UK
| | - Sacha J Howell
- 3The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX UK.,4Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Ian M Frayling
- 5All-Wales Medical Genetics Service, Cardiff & Vale University Health Board, University Hospital of Wales, Cardiff, CF14 4XW UK.,6Institute of Medical Genetics, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Juha Peltonen
- 7Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
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42
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Isakov O, Wallis D, Evans DG, Ben-Shachar S. Exhaustive non-synonymous variants functionality prediction enables high resolution characterization of the neurofibromin architecture. EBioMedicine 2018; 36:508-516. [PMID: 30274822 PMCID: PMC6197713 DOI: 10.1016/j.ebiom.2018.09.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/11/2018] [Accepted: 09/21/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Neurofibromatosis type I (NF1) is caused by heterozygous loss-of-function variants in the NF1 gene encoding neurofibromin which serves as a tumor suppressor that inhibits RAS signaling and regulates cell proliferation and differentiation. While, the only well-established functional domain in the NF1 protein is the GAP-related domain (GRD), most of the identified non-truncating disease-causing variants are located outside of this domain, supporting the existence of other important disease-associated domains. Identifying these domains may reveal novel functions of NF1. METHODS By implementing inferential statistics combined with machine-learning methods, we developed a novel NF1-specific functional prediction model that focuses on nonsynonymous single nucleotide variants (SNVs). The model enables annotating all possible NF1 nonsynonymous variants, thus mapping the range of pathogenic non-truncating variants at the codon level across the NF1 gene. FINDINGS The generated model demonstrates high absolute prediction value for missense and splice-site variations (area under the ROC curve of 0.96) outperforming 14 other established models. By reviewing the entire dataset of nonsynonymous variants, two novel domains (Armadillo type fold 1 and 2) were identified as being associated with pathogenicity (OR 1.86; CI 1.04 to 3.34 and OR 2.08; CI 1.08 to 4.04, respectively; P < .05). Specific exons and codons associated with increased pathogenicity were also detected along the gene inside and outside the GRD domain. INTERPRETATION The developed model, enabled better prediction of pathogenicity for variants in NF1 gene, as well as elucidation of novel NF1-associated domains in addition to the GRD. FUND: This work was partially supported by the Kahn foundation. DGE is supported by the all Manchester NIHR Biomedical Research Centre (IS-brC-1215-20007).
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Affiliation(s)
- Ofer Isakov
- Department of Internal Medicine "T", Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Science, University of Manchester, Manchester University Hospitals NHS Foundation Trust, Manchester, UK.
| | - Shay Ben-Shachar
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Gilbert Israeli Neurofibromatosis Center, Tel-Aviv Medical Center, Tel-Aviv, Israel.
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McVeigh TP, Sundar R, Diamantis N, Kaye SB, Banerji U, Lopez JS, de Bono J, van der Graaf WTA, George AJ. The role of genomic profiling in adolescents and young adults (AYAs) with advanced cancer participating in phase I clinical trials. Eur J Cancer 2018; 95:20-29. [PMID: 29614442 PMCID: PMC6296443 DOI: 10.1016/j.ejca.2018.02.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/25/2018] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Adolescents and young adults (AYAs) diagnosed with cancer between ages 15-39 years may harbour germline variants associated with cancer predisposition. Such variants represent putative therapeutic targets, as may somatic variants in the tumour. Germline and tumour molecular profiling is increasingly utilised to facilitate personalisation of cancer treatment in such individuals. AIM Considering AYAs with advanced solid tumours managed in a specialist drug development unit (DDU), the aims of this study were to investigate the use and impact of: 1. Germline genetic assessment. 2. Tumour molecular profiling. METHODS AYAs treated in the DDU at the Royal Marsden Hospital between 2002 and 2016 were identified from departmental databases. Data regarding clinicopathological features, clinical assessments and germline and tumour genetic testing were retrieved by chart review. RESULTS The study cohort included 219 AYAs. Common cancer types included sarcoma (41, 19%); cervical (27, 12%); breast (25, 11%); ovarian (23, 11%) and colorectal (21, 10%) cancers. Germline testing was undertaken in 34 (16%) patients, 22 of whom carried a pathogenic variant. Using current testing criteria, an additional 32 (15%) would be eligible for germline testing based on their personal history of cancer alone. Tumour testing was undertaken in 46 (21%) individuals. Somatic mutations were commonly identified in TP53 13 (28%); PIK3CA (8, 18%); KRAS (4, 9%) and MET 5 (11%). DISCUSSION A significant proportion of AYAs with advanced cancer have targetable somatic or germline mutations. Consideration of familial risk factors and inclusion of germline testing wherever appropriate can complement tumour testing to optimise patient management and inform management of at-risk relatives.
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Affiliation(s)
| | - Raghav Sundar
- Drug Development Unit, Royal Marsden NHS Foundation Trust and the Institute of Cancer Research, London, UK; Department of Haematology-Oncology, National University Health System, Singapore
| | - Nikolaos Diamantis
- Drug Development Unit, Royal Marsden NHS Foundation Trust and the Institute of Cancer Research, London, UK
| | - Stan B Kaye
- Drug Development Unit, Royal Marsden NHS Foundation Trust and the Institute of Cancer Research, London, UK
| | - Udai Banerji
- Drug Development Unit, Royal Marsden NHS Foundation Trust and the Institute of Cancer Research, London, UK
| | - Juanita S Lopez
- Drug Development Unit, Royal Marsden NHS Foundation Trust and the Institute of Cancer Research, London, UK
| | - Johann de Bono
- Drug Development Unit, Royal Marsden NHS Foundation Trust and the Institute of Cancer Research, London, UK
| | | | - Angela J George
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK; Gynaecology Unit, Royal Marsden NHS Foundation Trust and the Institute of Cancer Research, London, UK
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44
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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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45
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Evans DGR, Salvador H, Chang VY, Erez A, Voss SD, Schneider KW, Scott HS, Plon SE, Tabori U. Cancer and Central Nervous System Tumor Surveillance in Pediatric Neurofibromatosis 1. Clin Cancer Res 2018; 23:e46-e53. [PMID: 28620004 DOI: 10.1158/1078-0432.ccr-17-0589] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 11/16/2022]
Abstract
Although the neurofibromatoses consist of at least three autosomal dominantly inherited disorders, neurofibromatosis 1 (NF1), neurofibromatosis 2 (NF2), and schwannomatosis, NF1 represents a multisystem pleiotropic condition very different from the other two. NF1 is a genetic syndrome first manifesting in childhood; affecting multiple organs, childhood development, and neurocognitive status; and presenting the clinician with often complex management decisions that require a multidisciplinary approach. Molecular genetic testing (see article for detailed discussion) is recommended to confirm NF1, particularly in children fulfilling only pigmentary features of the diagnostic criteria. Although cancer risk is not the major issue facing an individual with NF1 during childhood, the condition causes significantly increased malignancy risks compared with the general population. Specifically, NF1 is associated with highly elevated risks of juvenile myelomonocytic leukemia, rhabdomyosarcoma, and malignant peripheral nerve sheath tumor as well as substantial risks of noninvasive pilocytic astrocytoma, particularly optic pathway glioma (OPG), which represent a major management issue. Until 8 years of age, clinical assessment for OPG is advised every 6 to 12 months, but routine MRI assessment is not currently advised in asymptomatic individuals with NF1 and no signs of clinical visual pathway disturbance. Routine surveillance for other malignancies is not recommended, but clinicians and parents should be aware of the small risks (<1%) of certain specific individual malignancies (e.g., rhabdomyosarcoma). Tumors do contribute to both morbidity and mortality, especially later in life. A single whole-body MRI should be considered at transition to adulthood to assist in determining approaches to long-term follow-up. Clin Cancer Res; 23(12); e46-e53. ©2017 AACRSee all articles in the online-only CCR Pediatric Oncology Series.
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Affiliation(s)
- D Gareth R Evans
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, United Kingdom.
- Manchester Academic Health Science Centre, Saint Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Hector Salvador
- Department of Pediatric Onco-Hematology and Developmental Tumor Biology Laboratory, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Vivian Y Chang
- Department of Pediatrics, Division of Pediatric Hematology-Oncology Children's Discovery and Innovation Institute, University of California, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California
- David Geffen School of Medicine, Los Angeles, California
| | - Ayelet Erez
- Weizmann Institute of Science, Rehovot, Israel
| | - Stephan D Voss
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kami Wolfe Schneider
- Hematology, Oncology, and Bone Marrow Transplant, University of Colorado Denver, Children's Hospital Colorado, Aurora, Colorado
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology & UniSA alliance, Adelaide, Australia
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Uri Tabori
- Division of Haematology/Oncology, University of Toronto, Toronto, Ontario, Canada
- Research Institute and The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
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Stivaros S, Garg S, Tziraki M, Cai Y, Thomas O, Mellor J, Morris AA, Jim C, Szumanska-Ryt K, Parkes LM, Haroon HA, Montaldi D, Webb N, Keane J, Castellanos FX, Silva AJ, Huson S, Williams S, Gareth Evans D, Emsley R, Green J. Randomised controlled trial of simvastatin treatment for autism in young children with neurofibromatosis type 1 (SANTA). Mol Autism 2018; 9:12. [PMID: 29484149 PMCID: PMC5824534 DOI: 10.1186/s13229-018-0190-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/12/2018] [Indexed: 11/24/2022] Open
Abstract
Background Neurofibromatosis 1 (NF1) is a monogenic model for syndromic autism. Statins rescue the social and cognitive phenotype in animal knockout models, but translational trials with subjects > 8 years using cognition/behaviour outcomes have shown mixed results. This trial breaks new ground by studying statin effects for the first time in younger children with NF1 and co-morbid autism and by using multiparametric imaging outcomes. Methods A single-site triple-blind RCT of simvastatin vs. placebo was done. Assessment (baseline and 12-week endpoint) included peripheral MAPK assay, awake magnetic resonance imaging spectroscopy (MRS; GABA and glutamate+glutamine (Glx)), arterial spin labelling (ASL), apparent diffusion coefficient (ADC), resting state functional MRI, and autism behavioural outcomes (Aberrant Behaviour Checklist and Clinical Global Impression). Results Thirty subjects had a mean age of 8.1 years (SD 1.8). Simvastatin was well tolerated. The amount of imaging data varied by test. Simvastatin treatment was associated with (i) increased frontal white matter MRS GABA (t(12) = - 2.12, p = .055), GABA/Glx ratio (t(12) = - 2.78, p = .016), and reduced grey nuclei Glx (ANCOVA p < 0.05, Mann-Whitney p < 0.01); (ii) increased ASL perfusion in ventral diencephalon (Mann-Whitney p < 0.01); and (iii) decreased ADC in cingulate gyrus (Mann-Whitney p < 0.01). Machine-learning classification of imaging outcomes achieved 79% (p < .05) accuracy differentiating groups at endpoint against chance level (64%, p = 0.25) at baseline. Three of 12 (25%) simvastatin cases compared to none in placebo met 'clinical responder' criteria for behavioural outcome. Conclusions We show feasibility of peripheral MAPK assay and autism symptom measurement, but the study was not powered to test effectiveness. Multiparametric imaging suggests possible simvastatin effects in brain areas previously associated with NF1 pathophysiology and the social brain network. Trial registration EU Clinical Trial Register (EudraCT) 2012-005742-38 (www.clinicaltrialsregister.eu).
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Affiliation(s)
- Stavros Stivaros
- Academic Unit of Paediatric Radiology, Royal Manchester Children’s Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Shruti Garg
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Greater Manchester Mental Health NHS Foundation Trust, Room 3.311, Jean McFarlane Building, Oxford Road, Manchester, M13 9PL UK
| | - Maria Tziraki
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Ying Cai
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences and Psychology, Integrative Center for Learning and Memory, Brain Research Institute, Brain Research Institute, University of California, California, LA 90095 USA
| | - Owen Thomas
- Academic Unit of Radiology, Salford Royal Foundation NHS Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Joseph Mellor
- Computer Science, University of Manchester, Manchester, UK
| | - Andrew A. Morris
- Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Carly Jim
- Manchester Metropolitan University, Manchester, UK
| | - Karolina Szumanska-Ryt
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Laura M Parkes
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Hamied A. Haroon
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Daniela Montaldi
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Nicholas Webb
- Department of Paediatric Nephrology, Royal Manchester Children’s Hospital, Manchester University NHS Foundation Trust, Academic Health Sciences Centre, Manchester, UK
| | - John Keane
- Computer Science, University of Manchester, Manchester, UK
| | - Francisco X. Castellanos
- Hassenfeld Children’s Hospital at NYU Langone, Nathan S. Kline Institute for Psychiatric Research, New York, USA
| | - Alcino J. Silva
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences and Psychology, Integrative Center for Learning and Memory, Brain Research Institute, Brain Research Institute, University of California, California, LA 90095 USA
| | - Sue Huson
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Academic Health Sciences Centre, Manchester, UK
| | - Stephen Williams
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - D. Gareth Evans
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Academic Health Sciences Centre, Manchester, UK
| | - Richard Emsley
- Centre for Biostatistics, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jonathan Green
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Greater Manchester Mental Health NHS Foundation Trust, Room 3.311, Jean McFarlane Building, Oxford Road, Manchester, M13 9PL UK
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Ullman D, Baumgartner E, Wnukowski N, Koenig G, Mikhail FM, Pavlidakey P, Peker D. Therapy-associated myelodysplastic syndrome with monosomy 7 arising in a Muir-Torre Syndrome patient carrying SETBP1 mutation. Mol Clin Oncol 2018; 8:306-309. [PMID: 29435294 DOI: 10.3892/mco.2017.1532] [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: 09/13/2017] [Accepted: 11/30/2017] [Indexed: 11/06/2022] Open
Abstract
Muir-Torre Syndrome (MTS) is a rare hereditary autosomal dominant cancer syndrome and is linked to hereditary non-polyposis colorectal carcinoma (Lynch Syndrome). Individuals develop various skin neoplasms in addition to colorectal, endometrial and upper gastrointestinal malignancies. Therapy-associated myelodysplastic syndrome (T-MDS) is an aggressive hematologic malignancy and is considered a pre-leukemic phase. T-MDS is associated with prior exposure to chemo- and radiotherapy that potentially results in DNA damage. The current case report presents a 74-year-old male MTS patient with prior history of solid tumors and radiation therapy with new onset cytopenia. A subsequent bone marrow biopsy revealed multilineage dysplasia with a high blast count and a diagnosis of high grade T-MDS was rendered. FISH and G-banded karyotype analyses revealed 5q deletion and monosomy 7. This is a unique case of T-MDS arising in the setting of MTS. Secondary malignancies including MDS and acute leukemia may occur in cancer survivors and are often associated with an unfavorable prognosis. This case demonstrates the need to be aware of the risk of secondary hematologic malignancies in cancer patients and a thorough clinical and lab work-up are warranted in patients with persistent or transfusion requiring cytopenia(s).
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Affiliation(s)
- David Ullman
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Erin Baumgartner
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Nicholas Wnukowski
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Gabe Koenig
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Peter Pavlidakey
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Deniz Peker
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
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48
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De Sousa SMC, Hardy TSE, Scott HS, Torpy DJ. Genetic Testing in Endocrinology. Clin Biochem Rev 2018; 39:17-28. [PMID: 30072819 PMCID: PMC6069737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The recent genomic revolution, characterised by surges in the number of available genetic tests and known genetic associations, calls for improved genetic literacy amongst medical scientists and clinicians. This has been driven by next generation sequencing, a technology allowing multiple genes to be sequenced in parallel, thereby reducing the time and financial costs associated with genetic testing in both research and clinical settings. Endocrinology is an intuitive setting in which to consider the principles of genetic testing because endocrine disorders are due to defects in circumscribed pathways, providing clues to candidate genes. This article discusses genetic testing in contemporary endocrine practice with reference to examples of endocrine genetic disorders or multisystem genetic disorders with endocrine manifestations. Monogenic disorders are prioritised as these form the bulk of endocrine genetic disorders and the associated genetic testing is readily understandable, clinically available and practice-changing. Although it remains true that genetic testing should be embarked upon only if the result will alter management, the clinical utility of genetic testing is often underestimated and there are expanding indications for genetic testing across all areas of endocrinology.
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Affiliation(s)
- Sunita MC De Sousa
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia
| | - Tristan SE Hardy
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia
- Repromed, Dulwich, SA, Australia
| | - Hamish S Scott
- School of Medicine, University of Adelaide, Adelaide, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - David J Torpy
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia
- School of Medicine, University of Adelaide, Adelaide, Australia
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Howell SJ, Hockenhull K, Salih Z, Evans DG. Increased risk of breast cancer in neurofibromatosis type 1: current insights. BREAST CANCER-TARGETS AND THERAPY 2017; 9:531-536. [PMID: 28860858 PMCID: PMC5573065 DOI: 10.2147/bctt.s111397] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant condition caused by mutation/deletion of the NF1 gene. The gene product, neurofibromin, is a tumor suppressor which represses the activity of the Ras oncogene. Central nervous system (CNS) tumors have long been associated with NF1, but their association with several other malignancies has been demonstrated. In this review, we summarize the epidemiological data that irrefutably support a link between NF1 and an increased risk of early-onset breast cancer, to levels at which annual mammography is currently recommended in national high-risk screening programs. We discuss the reasons for the observed adverse breast cancer prognosis in NF1 cases, including late presentation and more aggressive tumor subtypes, and recommend that a collaborative breast screening study be initiated to better serve this currently underserved population of women.
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Affiliation(s)
- Sacha J Howell
- Department of Medical Oncology, The Christie NHS Foundation Trust
| | | | - Zena Salih
- Department of Medical Oncology, The Christie NHS Foundation Trust
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre.,Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
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50
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Abstract
Background Neurofibromatosis type 1 (NF1: Online Mendelian Inheritance in Man (OMIM) #162200) is an autosomal dominantly inherited tumour predisposition syndrome. Heritable constitutional mutations in the NF1 gene result in dysregulation of the RAS/MAPK pathway and are causative of NF1. The major known function of the NF1 gene product neurofibromin is to downregulate RAS. NF1 exhibits variable clinical expression and is characterized by benign cutaneous lesions including neurofibromas and café-au-lait macules, as well as a predisposition to various types of malignancy, such as breast cancer and leukaemia. However, acquired somatic mutations in NF1 are also found in a wide variety of malignant neoplasms that are not associated with NF1. Main body Capitalizing upon the availability of next-generation sequencing data from cancer genomes and exomes, we review current knowledge of somatic NF1 mutations in a wide variety of tumours occurring at a number of different sites: breast, colorectum, urothelium, lung, ovary, skin, brain and neuroendocrine tissues, as well as leukaemias, in an attempt to understand their broader role and significance, and with a view ultimately to exploiting this in a diagnostic and therapeutic context. Conclusion As neurofibromin activity is a key to regulating the RAS/MAPK pathway, NF1 mutations are important in the acquisition of drug resistance, to BRAF, EGFR inhibitors, tamoxifen and retinoic acid in melanoma, lung and breast cancers and neuroblastoma. Other curiosities are observed, such as a high rate of somatic NF1 mutation in cutaneous melanoma, lung cancer, ovarian carcinoma and glioblastoma which are not usually associated with neurofibromatosis type 1. Somatic NF1 mutations may be critical drivers in multiple cancers. The mutational landscape of somatic NF1 mutations should provide novel insights into our understanding of the pathophysiology of cancer. The identification of high frequency of somatic NF1 mutations in sporadic tumours indicates that neurofibromin is likely to play a critical role in development, far beyond that evident in the tumour predisposition syndrome NF1.
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