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Revencu N, Eijkelenboom A, Bracquemart C, Alhopuro P, Armstrong J, Baselga E, Cesario C, Dentici ML, Eyries M, Frisk S, Karstensen HG, Gene-Olaciregui N, Kivirikko S, Lavarino C, Mero IL, Michiels R, Pisaneschi E, Schönewolf-Greulich B, Wieland I, Zenker M, Vikkula M. Assessment of gene-disease associations and recommendations for genetic testing for somatic variants in vascular anomalies by VASCERN-VASCA. Orphanet J Rare Dis 2024; 19:213. [PMID: 38778413 PMCID: PMC11110196 DOI: 10.1186/s13023-024-03196-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Vascular anomalies caused by somatic (postzygotic) variants are clinically and genetically heterogeneous diseases with overlapping or distinct entities. The genetic knowledge in this field is rapidly growing, and genetic testing is now part of the diagnostic workup alongside the clinical, radiological and histopathological data. Nonetheless, access to genetic testing is still limited, and there is significant heterogeneity across the approaches used by the diagnostic laboratories, with direct consequences on test sensitivity and accuracy. The clinical utility of genetic testing is expected to increase progressively with improved theragnostics, which will be based on information about the efficacy and safety of the emerging drugs and future molecules. The aim of this study was to make recommendations for optimising and guiding the diagnostic genetic testing for somatic variants in patients with vascular malformations. RESULTS Physicians and lab specialists from 11 multidisciplinary European centres for vascular anomalies reviewed the genes identified to date as being involved in non-hereditary vascular malformations, evaluated gene-disease associations, and made recommendations about the technical aspects for identification of low-level mosaicism and variant interpretation. A core list of 24 genes were selected based on the current practices in the participating laboratories, the ISSVA classification and the literature. In total 45 gene-phenotype associations were evaluated: 16 were considered definitive, 16 strong, 3 moderate, 7 limited and 3 with no evidence. CONCLUSIONS This work provides a detailed evidence-based view of the gene-disease associations in the field of vascular malformations caused by somatic variants. Knowing both the gene-phenotype relationships and the strength of the associations greatly help laboratories in data interpretation and eventually in the clinical diagnosis. This study reflects the state of knowledge as of mid-2023 and will be regularly updated on the VASCERN-VASCA website (VASCERN-VASCA, https://vascern.eu/groupe/vascular-anomalies/ ).
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Affiliation(s)
- Nicole Revencu
- Center for Human Genetics, Cliniques universitaires Saint-Luc, University of Louvain, VASCERN VASCA European Reference Centre, Brussels, Belgium
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud University Medical Center, VASCERN VASCA European Reference Centre, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Claire Bracquemart
- Normandie Univ, UNICAEN, Service de Génétique, CHU Caen Normandie, BIOTARGEN EA 7450, VASCERN VASCA European Reference Centre, Caen, 14000, France
| | - Pia Alhopuro
- HUS Diagnostic Center, Laboratory of Genetics, University of Helsinki and Helsinki University Hospital, VASCERN VASCA European Reference Centre, Helsinki, Finland
| | - Judith Armstrong
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, CIBER-ER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III (ISCIII), Madrid, and Genomic Unit, Molecular and Genetic Medicine Section, Hospital Sant Joan de Déu, VASCERN VASCA European Reference Centre, Barcelona, Spain
| | - Eulalia Baselga
- Department of Dermatology, Hospital Sant Joan de Deu, VASCERN VASCA European Reference Centre, Barcelona, Spain
| | - Claudia Cesario
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital and Research Institute, IRCCS, VASCERN VASCA European Reference Centre, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, VASCERN VASCA European Reference Centre, 00165, Rome, Italy
| | - Melanie Eyries
- Sorbonne Université, Département de Génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, VASCERN VASCA European Reference Centre, Paris, France
| | - Sofia Frisk
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, VASCERN VASCA European Reference Centre, Stockholm, Sweden
| | - Helena Gásdal Karstensen
- Department of Genetics, Center of Diagnostics, Copenhagen University Hospital - Rigshospitalet, VASCERN VASCA European Reference Centre, Copenhagen, Denmark
| | - Nagore Gene-Olaciregui
- Laboratory of Molecular Oncology, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, VASCERN VASCA European Reference Centre, Barcelona, Spain
| | - Sirpa Kivirikko
- Department of Clinical Genetics, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, VASCERN VASCA European Reference Centre, Helsinki, Finland
| | - Cinzia Lavarino
- Laboratory of Molecular Oncology, Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, VASCERN VASCA European Reference Centre, Barcelona, Spain
| | - Inger-Lise Mero
- Department of Medical Genetics, Oslo University Hospital, VASCERN VASCA European Reference Centre, Oslo, Norway
| | - Rodolphe Michiels
- Center for Human Genetics, Cliniques universitaires Saint-Luc, University of Louvain, VASCERN VASCA European Reference Centre, Brussels, Belgium
| | - Elisa Pisaneschi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital and Research Institute, IRCCS, VASCERN VASCA European Reference Centre, Rome, Italy
| | - Bitten Schönewolf-Greulich
- Department of Genetics, Center of Diagnostics, Copenhagen University Hospital - Rigshospitalet, VASCERN VASCA European Reference Centre, Copenhagen, Denmark
| | - Ilse Wieland
- Institute of Human Genetics, University Hospital Otto-Von-Guericke-University, Magdeburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Otto-Von-Guericke-University, Magdeburg, Germany
| | - Miikka Vikkula
- Center for Vascular Anomalies, Cliniques Universitaires Saint-Luc, Brussels, Belgium.
- Human Molecular Genetics , de Duve Institute, University of Louvain, VASCERN VASCA European Reference Centre, Brussels, Belgium.
- WELBIO Department, WEL Research Institute, Avenue Pasteur, 6, 1300, Wavre, Belgium.
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Wang X, Li H, Luo H, Zou Y, Li H, Qin Y, Song J. Evaluating ClinGen variant curation expert panels' application of PVS1 code. Eur J Med Genet 2024; 67:104909. [PMID: 38199457 DOI: 10.1016/j.ejmg.2024.104909] [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: 04/17/2023] [Revised: 08/02/2023] [Accepted: 01/07/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND The 2015 American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines articulates that the effects of certain types of variants on gene function can often be seen as a complete absence of the gene product by leading to a lack of transcription or nonsense-mediated decay(NMD). However, detailed information considering different types of loss of function(LOF) variants, refined steps assimilating details concerning location of variant, changes in strength levels, NMD boundary, or any additional information pointing to a true null effect, were all left to expert judgement. As part of its Clinical Genome Resource (ClinGen) initiative, Variant Curation Expert Panels (VCEPs) are designated to make gene/disease-centric specifications in accordance with the ACMG/AMP guidelines, including a more detailed definition of what constitutes an appropriate LOF evidence. Our goal was to evaluate the current LOF guidelines developed by the VCEPs and analyse the prior curated variants concerning the PVS1 criteria, bringing people occupied in genetic data analysis a comprehensive understanding of this code. METHODS Our study evaluated 7 VCEPs for their LOF criteria (PVS1). Subsequently, we assessed the predictive criteria by considering the underlying disease mechanism, protein transcript, and variant types delineated. Then, we meticulously curated the LOF evidence referenced by each VCEP in their preliminary variant classification, thereby scrutinizing the recommendations put forth by VCEPs and their application in the interpretation of the aforementioned predictive criteria. Based on these, an extensive curation of evidence summary considering PVS1 applied by VCEPs according to their classification of pilot variants for the purpose of analyzing VCEP criteria specifications and their use in the understanding of LOF was conducted. RESULTS We observed in this article that the VCEPs discussed followed the majority of Sequence Variant Interpretation (SVI) recommendations concerning the application of this LOF criteria, except for some disease/gene specific considerations. We highlighted the wide range of PVS1 strength levels approved by VCEP, reflecting the diversity of evidence for each variants type. In addition, we observed substantial differences in the approach used to determine relative strengths for different types of null variants and in the attitude towards these principles concerning variant location, NMD and influence to protein function between VCEPs. CONCLUSIONS It is difficult to understand the intricacies of the predictive data(PVS1), which often requires expert-level knowledge of disease/gene. The VCEP criteria specifications for the predictive evidence play an important role in making it more accessible for the curators to apply the predictive data by providing details concerning this complex criteria. Despite this, we believe there is a need for more guidance on standardizing this process and ensuring consistency in the application of this predictive evidence.
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Affiliation(s)
- Xiaoyan Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Haibo Li
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, 339 Liuting St, Ningbo City, Zhejiang Province, China
| | - Haiyan Luo
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yongyi Zou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Haoxian Li
- Center of Medical Genetics, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong, China
| | - Yayun Qin
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China.
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Straka B, Splitkova B, Vlckova M, Tesner P, Rezacova H, Krskova L, Koblizek M, Kyncl M, Maulisova A, Bukacova K, Uhrova-Meszarosova A, Musilova A, Kudr M, Ebel M, Belohlavkova A, Jahodova A, Liby P, Tichy M, Jezdik P, Zamecnik J, Aronica E, Krsek P. Genetic testing in children enrolled in epilepsy surgery program. A real-life study. Eur J Paediatr Neurol 2023; 47:80-87. [PMID: 37812946 DOI: 10.1016/j.ejpn.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
OBJECTIVE Although genetic causes of drug-resistant focal epilepsy and selected focal malformations of cortical development (MCD) have been described, a limited number of studies comprehensively analysed genetic diagnoses in patients undergoing pre-surgical evaluation, their outcomes and the effect of genetic diagnosis on surgical strategy. METHODS We analysed a prospective cohort of children enrolled in epilepsy surgery program over January 2018-July 2022. The majority of patients underwent germline and/or somatic genetic testing. We searched for predictors of surgical outcome and positive result of germline genetic testing. RESULTS Ninety-five patients were enrolled in epilepsy surgery program and 64 underwent resective epilepsy surgery. We ascertained germline genetic diagnosis in 13/74 patients having underwent germline gene testing (pathogenic or likely pathogenic variants in CHRNA4, NPRL3, DEPDC5, FGF12, GRIA2, SZT2, STXBP1) and identified three copy number variants. Thirty-five patients underwent somatic gene testing; we detected 10 pathogenic or likely pathogenic variants in genes SLC35A2, PTEN, MTOR, DEPDC5, NPRL3. Germline genetic diagnosis was significantly associated with the diagnosis of focal epilepsy with unknown seizure onset. SIGNIFICANCE Germline and somatic gene testing can ascertain a definite genetic diagnosis in a significant subgroup of patients in epilepsy surgery programs. Diagnosis of focal genetic epilepsy may tip the scales against the decision to proceed with invasive EEG study or surgical resection; however, selected patients with genetic focal epilepsies associated with MCD may benefit from resective epilepsy surgery and therefore, a genetic diagnosis does not disqualify patients from presurgical evaluation and epilepsy surgery.
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Affiliation(s)
- Barbora Straka
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Barbora Splitkova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Marketa Vlckova
- Department of Biology and Medical Genetics, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Pavel Tesner
- Department of Biology and Medical Genetics, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Hana Rezacova
- Department of Biology and Medical Genetics, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Lenka Krskova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Miroslav Koblizek
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Martin Kyncl
- Department of Radiology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Alice Maulisova
- Department of Clinical Psychology, Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Katerina Bukacova
- Department of Clinical Psychology, Motol University Hospital, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Anna Uhrova-Meszarosova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Alena Musilova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Martin Kudr
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Matyas Ebel
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Anezka Belohlavkova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Alena Jahodova
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Petr Liby
- Department of Neurosurgery, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Michal Tichy
- Department of Neurosurgery, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Petr Jezdik
- Faculty of Electrical Engineering, Department of Circuit Theory, Czech Technical University in Prague, Technicka 2, Praha 6, 166 27, Czech Republic.
| | - Josef Zamecnik
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
| | - Eleonora Aronica
- Amsterdam UMC Location University of Amsterdam, Department of Neuropathology, Amsterdam Neuroscience, the Netherlands; Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands.
| | - Pavel Krsek
- Department of Paediatric Neurology, Motol Epilepsy Center, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Full Member of the ERN EpiCARE, V Uvalu 84, 15006, Prague, Czech Republic.
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