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Mougel G, Mohamed A, Burnichon N, Giraud S, Pigny P, Bressac-de Paillerets B, Mirebeau-Prunier D, Buffet A, Savagner F, Romanet P, Arlot Y, Gardie B, Gimenez-Roqueplo AP, Beroud C, Richard S, Barlier A. Update of the UMD-VHL database: classification of 164 challenging variants based on genotype-phenotype correlation among 605 entries. J Med Genet 2024; 61:378-384. [PMID: 37979962 DOI: 10.1136/jmg-2023-109550] [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: 07/31/2023] [Accepted: 10/28/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND The von Hippel-Lindau (VHL) disease is a hereditary tumour syndrome caused by germline mutations in VHL tumour suppressor gene. The identification of VHL variants requires accurate classification which has an impact on patient management and genetic counselling. METHODS The TENGEN (French oncogenetics network of neuroendocrine tumors) and PREDIR (French National Cancer Institute network for Inherited predispositions to kidney cancer) networks have collected VHL genetic variants and clinical characteristics of all VHL-suspected patients analysed from 2003 to 2021 by one of the nine laboratories performing VHL genetic testing in France. Identified variants were registered in a locus-specific database, the Universal Mutation Database-VHL database (http://www.umd.be/VHL/). RESULTS Here we report the expert classification of 164 variants, including all missense variants (n=124), all difficult interpretation variants (n=40) and their associated phenotypes. After initial American College of Medical Genetics classification, first-round classification was performed by the VHL expert group followed by a second round for discordant and ambiguous cases. Overall, the VHL experts modified the classification of 87 variants including 30 variants of uncertain significance that were as (likely)pathogenic variants for 19, and as likely benign for 11. CONCLUSION Consequently, this work has allowed the diagnosis and influenced the genetic counselling of 45 VHL-suspected families and can benefit to the worldwide VHL community, through this review.
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Affiliation(s)
- Gregory Mougel
- Aix Marseille Univ, APHM, INSERM, MMG, U1251, GEnOPé Departement, M2GM, Timone Hospital, Marseille, France
| | - Amira Mohamed
- APHM, GEnOPé Department, M2GM, Timone Hospital, Marseille, France
| | - Nelly Burnichon
- Département de Médecine Génomique des Tumeurs et des Cancers, Hôpital européen Georges Pompidou, Assistance Publique Hôpitaux de Paris, Université Paris Cité, Inserm, PARCC, Paris, France
| | - Sophie Giraud
- Genetics Department, Hospices Civils de Lyon (HCL), University Hospital, East Pathology Center, Lyon, France
| | - Pascal Pigny
- Service de Biochimie et Biologie Moléculaire « Hormonologie, Métabolisme-Nutrition, Oncologie », Centre de Biologie Pathologie, CHU Lille, Bd du Pr J Leclercq, Lille, France
| | - Brigitte Bressac-de Paillerets
- Service de Genetique, Département de Biologie et Pathologies Médicales, Gustave Roussy; INSERM U1279, Université Paris-Saclay, Villejuif Cedex, France
| | - Delphine Mirebeau-Prunier
- Département de Biochimie et Génétique, Service de Biochimie et Biologie Moléculaire, CHU d'Angers, University of Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFRICAT, Angers, France
| | - Alexandre Buffet
- Département de Médecine Génomique des Tumeurs et des Cancers, Hôpital européen Georges Pompidou, Assistance Publique Hôpitaux de Paris, Université Paris Cité, Inserm, PARCC, Paris, France
| | - Frédérique Savagner
- Laboratoire de Biochimie, Institut Fédératif de Biologie, CHU Toulouse; Inserm UMR1297, I2MC, Toulouse, France
| | - Pauline Romanet
- Aix Marseille Univ, APHM, INSERM, MMG, U1251, GEnOPé Departement, M2GM, Timone Hospital, Marseille, France
| | - Yannick Arlot
- CNRS UMR6290, Université Rennes 1, SFR-UMS CNRS 3480, INSERM 018, Rennes, France
| | - Betty Gardie
- Ecole Pratique des Hautes Etudes, EPHE, Université PSL; Université de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Anne-Paule Gimenez-Roqueplo
- Département de Médecine Génomique des Tumeurs et des Cancers, Hôpital européen Georges Pompidou, Assistance Publique Hôpitaux de Paris, Université Paris Cité, Inserm, PARCC, Paris, France
| | - Christophe Beroud
- Department of Genetics, M2GM, Timone Hospital, Aix Marseille Univ, APHM, INSERM, MMG, U1251 Bioinformatic Team, Marseille, France
| | - Stephane Richard
- Ecole Pratique des Hautes Etudes, EPHE, Université PSL, France, UMR 9019-CNRS, Gustave Roussy Cancer Campus, Villejuif, France et Service d'Urologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bicêtre, Le Kremlin-Bicêtre, Paris, France
- Réseau National pour Cancers rares de l'Adulte PREDIR labellisé par l'INCa, Assistance Publique-Hôpitaux de Paris, Hôpital Bicêtre, Paris, France
| | - Anne Barlier
- Aix Marseille Univ, APHM, INSERM, MMG, U1251, GEnOPé Departement, M2GM, Timone Hospital, Marseille, France
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Taher MM, Bantan NA, Alwalily MH, Saeed M, Taher NM, Bouzidi M, Jastania RA, Balkhoyour KB. Supratentorial Sporadic Hemangioblastoma: A Case Report With Mutation Profiling Using Next-Generation DNA Sequencing. Cureus 2023; 15:e39818. [PMID: 37273678 PMCID: PMC10233511 DOI: 10.7759/cureus.39818] [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] [Accepted: 05/31/2023] [Indexed: 06/06/2023] Open
Abstract
The present study aimed to determine genomic changes in sporadic intracranial hemangioblastoma (HBL), and the mutation patterns were analyzed using next-generation DNA sequencing (NGS). In this NGS analysis of the HBL tumor, 67 variants of 41 genes were identified. Of these, 64 were single-nucleotide variants (SNVs), two were exonic insertions and deletions (INDEL), and one was an intronic INDEL. In total, 15 were missense exonic variants, including an insertion variant in the NRAS gene, c.1_2insA, and a deletion variant, c.745delT, in the HNF1A gene, both of these mutations produced a termination codon. Other exonic missense variants found in the tumor were CTNNB1, FGFR3, KDR, SMO, HRAS, RAI1, and a TP53 variant (c.430C>G). Moreover, the results of the present study revealed a novel variant, c.430C>G, in TP53 and two missense variants of SND1 (c.1810G>C and c.1814G>C), which were also novel. ALK (rs760315884) and FGFR2 (rs1042522) missense variants were reported previously. Notably, a total of 10 previously reported single-nucleotide polymorphisms (SNPs) were found in this tumor in genes including MLH1 (rs769364808), FGFR3 (rs769364808), two variants (rs1873778 and rs2228230) in PDGFRA, KIT (rs55986963), APC (rs41115), and RET (rs1800861). The results of this study revealed a synonymous mutation (SNP) in c.1104 G>T; p. (Ser368Ser) in the MLH1 gene. In this amino acid (AA) codon, two other variants are also known to cause missense substitutions, c.1103C>G; p. (Ser368Trp); COSM6986674) and c.1103C>T; p.(Ser368Leu; COSM3915870), were found in hematopoietic and urinary tract tissue, respectively. However, three SNPs found in genes such as ALK, KDR, and ABL1 in the HBL tumor in this study were not reported in UCSC, COSMIC, and ClinVar databases. Additionally, 19 intronic variants were identified in this tumor. One intronic SNV was present in each of the following genes: EGFR, ERBB4, KDR, SMO, CDKN2B, PTEN, PTPN11, RB1, AKT1, and ERBB2. In PIK3CA and FBXL18 genes, two intronic variants were present, and in the SND1 gene, three intronic variants were detected in the HBL tumor presented in this study. Notably, only one of these was reported in the catalog of somatic mutations in cancer. Only one 3'-untranslated region (UTR) insertion variant in the NRAS gene (c.*2010T>AT) was detected in the tumor of the present study, and this was a splice site acceptor. A TP53 intronic mutation (c.782+1G>T) was the only pathogenic splice_donor_variant found in this HBL tumor. The frequency of variants and Phred scores were markedly high, and the p-values were significant for all of the aforementioned mutations. In summary, a total of 15 missense, 10 synonymous, and 19 intronic variants were identified in the HBL tumor. Results of the present study detected one novel insertion in NRAS and one novel deletion in HNF1A genes, a novel missense variant in the TP53 gene, and two novel missense variants of SND1. Hotspot mutations in other cancer driver genes, such as PTEN, ATM, SMAD4, SMARCB1, STK11, NPM1, CDKN2A, and EGFR, which are frequently affected in gliomas, were not found in the tumor of the present study. Future studies should aim to validate oncogenic mutations that may act as novel targets for the treatment of these tumors.
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Affiliation(s)
- Mohiuddin M Taher
- Science and Technology Unit, Deanship of Scientific Research, Umm Al-Qura University, Makkah, SAU
- Department of Medical Genetics, Umm Al-Qura University College of Medicine, Makkah, SAU
| | - Najwa A Bantan
- Department of Radiology, Al-Noor Specialty Hospital, Makkah, SAU
| | | | - Muhammad Saeed
- Department of Radiology, Al-Noor Specialty Hospital, Makkah, SAU
| | - Nuha M Taher
- Department of Medical Genetics, Umm Al-Qura University College of Medicine, Makkah, SAU
| | - Meriem Bouzidi
- Department of Laboratory Medicine, Division of Histopathology, Al-Noor Specialty Hospital, Makkah, SAU
| | - Raid A Jastania
- Department of Pathology, Umm Al-Qura University College of Medicine, Makkah, SAU
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3
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Lagarde A, Mougel G, Coppin L, Haissaguerre M, Le Collen L, Mohamed A, Klein M, Odou MF, Tabarin A, Brixi H, Cuny T, Delemer B, Barlier A, Romanet P. Systematic detection of mosaicism by using digital NGS reveals three new MEN1 mosaicisms. Endocr Connect 2022; 11:e220093. [PMID: 36112497 PMCID: PMC9578105 DOI: 10.1530/ec-22-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/16/2022] [Indexed: 11/08/2022]
Abstract
Purpose Mosaicism is a feature of several inherited tumor syndromes. Only a few cases of mosaicism have been described in multiple endocrine neoplasia type 1 (MEN1). Next-generation sequencing (NGS) offers new possibilities for detecting mosaicism. Here, we report the first study to systematically look for MEN1 mosaicism, using blood DNA, in MEN1-suspected patients but without MEN1 pathogenic variants (PV) in a heterozygous state. Methods Digital targeted NGS, including unique molecular identifiers (UMIs), was performed in routine practice, and the analytic performance of this method was verified. Results Among a cohort of 119 patients harboring from 2 to 5 MEN1 lesions, we identified 3 patients with MEN1 mosaic PVs. The allele frequencies ranged from 2.3 to 9.5%. The detection rate of MEN1 mosaicism in patients bearing at least 3 MEN1 lesions was 17% (3/18). No cases were detected in patients with two lesions. Conclusion We report here three new cases with MEN1 mosaicism. This study examined the performance of UMI in the diagnosis of MEN1 mosaicism in routine practice, and our results underline that the frequency of mosaicism is probably underestimated in patients with suspected MEN1.
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Affiliation(s)
- Arnaud Lagarde
- Aix Marseille Univ, APHM, INSERM, MMG, Laboratory of Molecular Biology Hospital La Conception, Marseille, France
| | - Grégory Mougel
- Aix Marseille Univ, APHM, INSERM, MMG, Laboratory of Molecular Biology Hospital La Conception, Marseille, France
| | - Lucie Coppin
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 – CANTHER – Cancer – Heterogeneity Plasticity and Resistance to Therapies, Lille, France
| | - Magalie Haissaguerre
- Service d’Endocrinologie, Centre Hospitalier Universitaire, Hôpital du Haut Levêque, Pessac, France
| | - Lauriane Le Collen
- Endocrinology, Diabetology and Nutrition Unit, University Hospital of Reims, Reims, France
- Inserm/CNRS UMR 1283/8199, Pasteur Institute of Lille, EGID, Lille, France
| | - Amira Mohamed
- Laboratory of Molecular Biology, Hospital La Conception, APHM, Marseille, France
| | - Marc Klein
- Service Endocrinologie, CHU de Nancy, Hôpital de Brabois, Vandoeuvre-lès-Nancy, France
| | - Marie-Françoise Odou
- CHU Lille, Service de Biochimie et Biologie Moléculaire ‘Hormonologie, Métabolisme-Nutrition, Oncologie’, Lille, France
- Univ. Lille, Inserm, CHU Lille, U1286 – Infinite – Institute for Translational Research in Inflammation, Lille, France
| | - Antoine Tabarin
- Service d’Endocrinologie, Centre Hospitalier Universitaire, Hôpital du Haut Levêque, Pessac, France
| | - Hedia Brixi
- Department of Gastroenterology and Digestive Oncology, Reims University Hospital, Reims, France
| | - Thomas Cuny
- Aix Marseille Univ, APHM, INSERM, MMG, Department of Endocrinology, Hospital La Conception, Marseille, France
| | - Brigitte Delemer
- Endocrinology, Diabetology and Nutrition Unit, University Hospital of Reims, Reims, France
| | - Anne Barlier
- Aix Marseille Univ, APHM, INSERM, MMG, Laboratory of Molecular Biology Hospital La Conception, Marseille, France
| | - Pauline Romanet
- Aix Marseille Univ, APHM, INSERM, MMG, Laboratory of Molecular Biology Hospital La Conception, Marseille, France
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Abedalthagafi M. Commentary: Von Hippel-Lindau disease: A clinical and scientific review. Eur J Hum Genet 2022; 30:1103-1104. [PMID: 36221028 PMCID: PMC9553946 DOI: 10.1038/s41431-022-01172-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/27/2022] [Indexed: 11/07/2022] Open
Affiliation(s)
- Malak Abedalthagafi
- Genomics Research Department, King Fahad Medical City, Riyadh, Saudi Arabia.
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5
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Chen JL, Miller DT, Schmidt LS, Malkin D, Korf BR, Eng C, Kwiatkowski DJ, Giannikou K. Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk. Annu Rev Genomics Hum Genet 2022; 23:331-361. [PMID: 36044908 DOI: 10.1146/annurev-genom-120121-105450] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mosaic state arises when pathogenic variants are acquired in certain cell lineages during postzygotic development, and mosaic individuals may present with a generalized or localized phenotype. Here, we review the current state of knowledge regarding mosaicism for eight common tumor suppressor genes-NF1, NF2, TSC1, TSC2, PTEN, VHL, RB1, and TP53-and their related genetic syndromes/entities. We compare and discuss approaches for comprehensive diagnostic genetic testing, the spectrum of variant allele frequency, and disease severity. We also review affected individuals who have no mutation identified after conventional genetic analysis, as well as genotype-phenotype correlations and transmission risk for each tumor suppressor gene in full heterozygous and mosaic patients. This review provides new insight into similarities as well as marked differences regarding the appreciation of mosaicism in these tumor suppressor syndromes.
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Affiliation(s)
- Jillian L Chen
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Boston University School of Medicine, Boston, Massachusetts, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA;
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA;
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Wolters WPG, Dreijerink KMA, Giles RH, van der Horst‐Schrivers ANA, van Nesselrooij B, Zandee WT, Timmers HJLM, Seute T, de Herder WW, Verrijn Stuart AA, Kilic E, Brinkman WM, Zondervan PJ, Vandertop WP, Daniels AB, Wolbers T, Links TP, van Leeuwaarde RS. Multidisciplinary integrated care pathway for von Hippel-Lindau disease. Cancer 2022; 128:2871-2879. [PMID: 35579632 PMCID: PMC9542729 DOI: 10.1002/cncr.34265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/14/2022] [Accepted: 04/22/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND Clinical pathways are care plans established to describe essential steps in the care of patients with a specific clinical problem. They translate (inter)national guidelines into local applicable protocols and clinical practice. The purpose of this article is to establish a multidisciplinary integrated care pathway for specialists and allied health care professionals in caring for individuals with von Hippel-Lindau (VHL) disease. METHODS Using a modified Delphi consensus-making process, a multidisciplinary panel from 5 Dutch University Medical Centers produced an integrated care pathway relating to the provision of care for patients with VHL by medical specialists, specialized nurses, and associated health care professionals. Patient representatives cocreated the pathway and contributed quality criteria from the patients' perspective. RESULTS The panel agreed on recommendations for the optimal quality of care for individuals with a VHL gene mutation. These items were the starting point for the development of a patient care pathway. With international medical guidelines addressing the different VHL-related disorders, this article presents a patient care pathway as a flowchart that can be incorporated into VHL expertise clinics or nonacademic treatment clinics. CONCLUSIONS Medical specialists (internists, urologists, neurosurgeons, ophthalmologists, geneticists, medical oncologists, neurologists, gastroenterologists, pediatricians, and ear-nose-throat specialists) together with specialized nurses play a vital role alongside health care professionals in providing care to people affected by VHL and their families. This article presents a set of consensus recommendations, supported by organ-specific guidelines, for the roles of these practitioners in order to provide optimal VHL care. This care pathway can form the basis for the development of comprehensive, integrated pathways for multiple neoplasia syndromes.
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Affiliation(s)
- Wendy P. G. Wolters
- Department of Endocrine OncologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Koen M. A. Dreijerink
- Department of EndocrinologyAmsterdam University Medical CenterAmsterdamthe Netherlands
| | - Rachel H. Giles
- Dutch VHL OrganizationUtrechtthe Netherlands,International Kidney Cancer CoalitionAmsterdam‐Duivendrechtthe Netherlands
| | | | | | - Wouter T. Zandee
- Department of EndocrinologyUniversity Medical Center GroningenGroningenthe Netherlands
| | | | - Tatjana Seute
- Department of NeurologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Wouter W. de Herder
- Department of Internal MedicineErasmus Medical CenterRotterdamthe Netherlands
| | | | - Emine Kilic
- Department of OphthalmologyErasmus Medical CenterRotterdamthe Netherlands
| | - Willem M. Brinkman
- Department of Oncological UrologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | | | - W. Peter Vandertop
- Department of NeurosurgeryAmsterdam NeuroscienceAmsterdamthe Netherlands
| | - Anthony B. Daniels
- Division of Ocular Oncology and PathologyDepartment of Ophthalmology and Visual Sciences, Vanderbilt‐Ingram Cancer CenterVanderbilt University Medical CenterNashvilleTennessee
| | | | - Thera P. Links
- Department of EndocrinologyUniversity Medical Center GroningenGroningenthe Netherlands
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Coppin L, Giraud S, Pasmant E, Lagarde A, North MO, Le-Collen L, Aubert V, Mougel G, Ladsous M, Louboutin A, Brixi H, Haissaguerre M, Scheyer N, Klein M, Tabarin A, Delemer B, Barlier A, Odou MF, Romanet P. Multiple endocrine neoplasia type 1 caused by mosaic mutation: clinical follow-up and genetic counseling? Eur J Endocrinol 2022; 187:K1-K6. [PMID: 35521764 DOI: 10.1530/eje-22-0171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/04/2022] [Indexed: 11/08/2022]
Abstract
MEN1 is an autosomal dominant hereditary syndrome characterized by several endocrine tumors, in most cases affecting the parathyroid glands, pancreas, and anterior pituitary. It is the result of inactivating mutations in the tumor suppressor gene MEN1. More than 1300 different mutations have been identified in this gene. Mosaic MEN1 mutations have been previously described in only a few patients in the literature. In this paper, we provide a review of six cases of MEN1 mosaicism reported in the literature supplemented with six additional cases described by the French TENgen network of laboratories. This review highlights that (i) MEN1 mosaicism is not associated with a mild phenotype and results in the same natural history as heterozygous MEN1 mutation and (ii) that more systematic detection of MEN1 mosaic mutation enables improvements in both patient monitoring and genetic counseling.
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Affiliation(s)
- Lucie Coppin
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer - Heterogeneity Plasticity and Resistance to Therapies, Lille, France
| | - Sophie Giraud
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, Lyon, France
| | - Eric Pasmant
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP, Centre-Université de Paris, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, CARPEM, Paris, France
| | - Arnaud Lagarde
- Aix Marseille Univ, APHM, INSERM, MMG, Laboratory of Molecular Biology Hospital La Conception, Marseille, France
| | - Marie-Odile North
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP, Centre-Université de Paris, Paris, France
| | - Lauriane Le-Collen
- Endocrinology, Diabetology and Nutrition Unit, University Hospital of Reims, Reims, France
- Inserm/CNRS UMR 1283/8199, Pasteur Institute of Lille, EGID, Lille, France
| | | | - Grégory Mougel
- Genetics Department, Hospices Civils de LYON (HCL), University Hospital, East Pathology Center, Lyon, France
| | - Miriam Ladsous
- CHU Lille, Service d'Endocrinologie, Diabétologie, Métabolisme et Nutrition, Hôpital Claude Huriez, Lille, France
| | - Alyzée Louboutin
- CH Cornouaille Quimper - Service d'Endocrinologie, Quimper, France
| | - Hedia Brixi
- Department of Gastroenterology and Digestive Oncology, Reims University Hospital, Reims, France
| | - Magalie Haissaguerre
- Service d'Endocrinologie, Centre Hospitalier Universitaire, Hôpital du Haut Levêque, Pessac, France
| | - Nicolas Scheyer
- Service Endocrinologie, CHU de Nancy, Hôpital de Brabois, Vandoeuvre-lès-Nancy, France
| | - Marc Klein
- Service Endocrinologie, CHU de Nancy, Hôpital de Brabois, Vandoeuvre-lès-Nancy, France
| | - Antoine Tabarin
- Service d'Endocrinologie, Centre Hospitalier Universitaire, Hôpital du Haut Levêque, Pessac, France
| | - Brigitte Delemer
- Endocrinology, Diabetology and Nutrition Unit, University Hospital of Reims, Reims, France
| | - Anne Barlier
- Aix Marseille Univ, APHM, INSERM, MMG, Laboratory of Molecular Biology Hospital La Conception, Marseille, France
| | - Marie-Françoise Odou
- CHU Lille, Service de Biochimie et Biologie moléculaire 'Hormonologie, Métabolisme-Nutrition, Oncologie', Lille, France
- Univ. Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational Research in Inflammation, Lille, France
| | - Pauline Romanet
- Aix Marseille Univ, APHM, INSERM, MMG, Laboratory of Molecular Biology Hospital La Conception, Marseille, France
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8
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VHL mosaicism: the added value of multi-tissue analysis. NPJ Genom Med 2022; 7:21. [PMID: 35304467 PMCID: PMC8933488 DOI: 10.1038/s41525-022-00291-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/15/2022] [Indexed: 11/09/2022] Open
Abstract
Von Hippel-Lindau disease (VHL) is an autosomal dominant, inherited syndrome with variants in the VHL gene causing predisposition to multi-organ benign and malignant neoplasms. A germline VHL variant is identified in 95-100% of individuals with a clinical diagnosis of VHL. Here, we present the case of an individual with a clinical diagnosis of VHL disease where peripheral blood DNA analysis did not detect a VHL variant. Sequencing of four tumor tissues (ccRCC, pheochromocytoma, lung via sputum, liver) revealed a VHL c.593 T > C (p.Leu198Pro) variant at varying allele fractions (range: 10-55%) in all tissues. Re-examination of the peripheral blood sequencing data identified this variant at 6% allele fraction. Tumor analysis revealed characteristic cytomorphological, immunohistochemical reactivity for alpha-inhibin, and CAIX, and reduced pVHL reactivity supported VHL-related pseudohypoxia. This report of a rare case of VHL mosaicism highlights the value of tissue testing in VHL variant negative cases.
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9
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Chevalier B, Dupuis H, Jannin A, Lemaitre M, Do Cao C, Cardot-Bauters C, Espiard S, Vantyghem MC. Phakomatoses and Endocrine Gland Tumors: Noteworthy and (Not so) Rare Associations. Front Endocrinol (Lausanne) 2021; 12:678869. [PMID: 34025587 PMCID: PMC8134657 DOI: 10.3389/fendo.2021.678869] [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: 03/10/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
Phakomatoses encompass a group of rare genetic diseases, such as von Hippel-Lindau syndrome (VHL), neurofibromatosis type 1 (NF1), tuberous sclerosis complex (TSC) and Cowden syndrome (CS). These disorders are due to molecular abnormalities on the RAS-PI3K-Akt-mTOR pathway for NF1, TSC and CS, and to hypoxia sensing for VHL. Phakomatoses share some phenotypic traits such as neurological, ophthalmological and cutaneous features. Patients with these diseases are also predisposed to developing multiple endocrine tissue tumors, e.g., pheochromocytomas/paragangliomas are frequent in VHL and NF1. All forms of phakomatoses except CS may be associated with digestive neuroendocrine tumors. More rarely, thyroid cancer and pituitary or parathyroid adenomas have been reported. These susceptibilities are noteworthy, because their occurrence rate, prognosis and management differ slightly from the sporadic forms. The aim of this review is to summarize current knowledge on endocrine glands tumors associated with VHL, NF1, TSC, and CS, especially neuroendocrine tumors and pheochromocytomas/paragangliomas. We particularly detail recent advances concerning prognosis and management, especially parenchyma-sparing surgery and medical targeted therapies such as mTOR, MEK and HIF-2 α inhibitors, which have shown truly encouraging results.
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Affiliation(s)
- Benjamin Chevalier
- Department of Endocrinology, Diabetology and Metabolism, Lille University Hospital, Lille, France
- University of Lille, Lille, France
| | - Hippolyte Dupuis
- Department of Endocrinology, Diabetology and Metabolism, Lille University Hospital, Lille, France
| | - Arnaud Jannin
- Department of Endocrinology, Diabetology and Metabolism, Lille University Hospital, Lille, France
- University of Lille, Lille, France
| | - Madleen Lemaitre
- Department of Endocrinology, Diabetology and Metabolism, Lille University Hospital, Lille, France
- University of Lille, Lille, France
| | - Christine Do Cao
- Department of Endocrinology, Diabetology and Metabolism, Lille University Hospital, Lille, France
| | - Catherine Cardot-Bauters
- Department of Endocrinology, Diabetology and Metabolism, Lille University Hospital, Lille, France
| | - Stéphanie Espiard
- Department of Endocrinology, Diabetology and Metabolism, Lille University Hospital, Lille, France
- University of Lille, Lille, France
- INSERM U1190, European Genomic Institute for Diabetes, Lille, France
| | - Marie Christine Vantyghem
- Department of Endocrinology, Diabetology and Metabolism, Lille University Hospital, Lille, France
- University of Lille, Lille, France
- INSERM U1190, European Genomic Institute for Diabetes, Lille, France
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10
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Doan RN, Miller MB, Kim SN, Rodin RE, Ganz J, Bizzotto S, Morillo KS, Huang AY, Digumarthy R, Zemmel Z, Walsh CA. MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC Med Genomics 2021; 14:47. [PMID: 33579278 PMCID: PMC7881461 DOI: 10.1186/s12920-021-00893-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/03/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mosaic mutations contribute to numerous human disorders. As such, the identification and precise quantification of mosaic mutations is essential for a wide range of research applications, clinical diagnoses, and early detection of cancers. Currently, the low-throughput nature of single allele assays (e.g., allele-specific ddPCR) commonly used for genotyping known mutations at very low alternate allelic fractions (AAFs) have limited the integration of low-level mosaic analyses into clinical and research applications. The growing importance of mosaic mutations requires a more rapid, low-cost solution for mutation detection and validation. METHODS To overcome these limitations, we developed Multiple Independent Primer PCR Sequencing (MIPP-Seq) which combines the power of ultra-deep sequencing and truly independent assays. The accuracy of MIPP-seq to quantifiable detect and measure extremely low allelic fractions was assessed using a combination of SNVs, insertions, and deletions at known allelic fractions in blood and brain derived DNA samples. RESULTS The Independent amplicon analyses of MIPP-Seq markedly reduce the impact of allelic dropout, amplification bias, PCR-induced, and sequencing artifacts. Using low DNA inputs of either 25 ng or 50 ng of DNA, MIPP-Seq provides sensitive and quantitative assessments of AAFs as low as 0.025% for SNVs, insertion, and deletions. CONCLUSIONS MIPP-Seq provides an ultra-sensitive, low-cost approach for detecting and validating known and novel mutations in a highly scalable system with broad utility spanning both research and clinical diagnostic testing applications. The scalability of MIPP-Seq allows for multiplexing mutations and samples, which dramatically reduce costs of variant validation when compared to methods like ddPCR. By leveraging the power of individual analyses of multiple unique and independent reactions, MIPP-Seq can validate and precisely quantitate extremely low AAFs across multiple tissues and mutational categories including both indels and SNVs. Furthermore, using Illumina sequencing technology, MIPP-seq provides a robust method for accurate detection of novel mutations at an extremely low AAF.
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Affiliation(s)
- Ryan N Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA. .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
| | - Michael B Miller
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sonia N Kim
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA.,Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Katherine S Morillo
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - August Yue Huang
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Reethika Digumarthy
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Zachary Zemmel
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA. .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA. .,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
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11
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Radtke HB, Lalor LE, Basel DG, Siegel DH. Clinical Implications of Mosaicism and Low-Level Mosaicism in Neurocutaneous Disorders. CURRENT GENETIC MEDICINE REPORTS 2020. [DOI: 10.1007/s40142-020-00193-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Abstract
Abstract
Purpose of Review
In this review, we discuss the key molecular and clinical developments in VHL disease that have the potential to impact on the natural history of the disease and improve patient outcomes.
Recent Findings
Identifiable mutations in VHL underlie most cases of VHL and define clear genotype-phenotype correlations. Detailed clinical and molecular characterisation has allowed the implementation of lifelong screening programmes that have improved clinical outcomes. Functional characterisation of the VHL protein complex has revealed its role in oxygen sensing and the mechanisms of tumourigenesis that are now being exploited to develop novel therapies for VHL and renal cancer.
Summary
The molecular and cellular landscape of VHL-associated tumours is revealing new opportunities to modify the natural history of the disease and develop therapies. Drugs are now entering clinical trials and combined with improved clinical and molecular diagnosis, and lifelong surveillance programmes, further progress towards reducing the morbidity and mortality associated with VHL disease is anticipated.
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13
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Kant B, Carbo EC, Kokmeijer I, Oosterman JJM, Frenkel J, Swertz MA, Ploos van Amstel JK, Aróstegui JI, Koudijs MJ, van Gijn ME. Gene Mosaicism Screening Using Single-Molecule Molecular Inversion Probes in Routine Diagnostics for Systemic Autoinflammatory Diseases. J Mol Diagn 2019; 21:943-950. [PMID: 31442672 DOI: 10.1016/j.jmoldx.2019.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/17/2019] [Accepted: 06/26/2019] [Indexed: 11/17/2022] Open
Abstract
Diagnosis of systemic autoinflammatory diseases (SAIDs) is often difficult to achieve and can delay the start of proper treatments and result in irreversible organ damage. In several patients with dominantly inherited SAID, postzygotic mutations have been detected as the disease-causing gene defects. Mutations with allele frequencies <5% have been detected, even in patients with severe phenotypes. Next-generation sequencing techniques are currently used to detect mutations in SAID-associated genes. However, even if the genomic region is highly covered, this approach is usually not able to distinguish low-grade postzygotic variants from background noise. We, therefore, developed a sensitive deep sequencing assay for mosaicism detection in SAID-associated genes using single-molecule molecular inversion probes. Our results show the accurate detection of postzygotic variants with allele frequencies as low as 1%. The probability of calling mutations with allele frequencies ≥3% exceeds 99.9%. To date, we have detected three patients with mosaicism, two carrying likely pathogenic NLRP3 variants and one carrying a likely pathogenic TNFRSF1A variant with an allele frequency of 1.3%, confirming the relevance of the technology. The assay shown herein is a flexible, robust, fast, cost-effective, and highly reliable method for mosaicism detection; therefore, it is well suited for routine diagnostics.
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Affiliation(s)
- Benjamin Kant
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Ellen C Carbo
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Iris Kokmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jelske J M Oosterman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joost Frenkel
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Morris A Swertz
- Genomics Coordination Center and Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | | | | | - Marco J Koudijs
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mariëlle E van Gijn
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
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