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Wright CF, Sharp LN, Jackson L, Murray A, Ware JS, MacArthur DG, Rehm HL, Patel KA, Weedon MN. Guidance for estimating penetrance of monogenic disease-causing variants in population cohorts. Nat Genet 2024; 56:1772-1779. [PMID: 39075210 DOI: 10.1038/s41588-024-01842-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/24/2024] [Indexed: 07/31/2024]
Abstract
Penetrance is the probability that an individual with a pathogenic genetic variant develops a specific disease. Knowing the penetrance of variants for monogenic disorders is important for counseling of individuals. Until recently, estimates of penetrance have largely relied on affected individuals and their at-risk family members being clinically referred for genetic testing, a 'phenotype-first' approach. This approach substantially overestimates the penetrance of variants because of ascertainment bias. The recent availability of whole-genome sequencing data in individuals from very-large-scale population-based cohorts now allows 'genotype-first' estimates of penetrance for many conditions. Although this type of population-based study can underestimate penetrance owing to recruitment biases, it provides more accurate estimates of penetrance for secondary or incidental findings. Here, we provide guidance for the conduct of penetrance studies to ensure that robust genotypes and phenotypes are used to accurately estimate penetrance of variants and groups of similarly annotated variants from population-based studies.
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Affiliation(s)
- Caroline F Wright
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK.
| | - Luke N Sharp
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - Leigh Jackson
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - Anna Murray
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - James S Ware
- National Heart and Lung Institute and MRC Laboratory of Medical Sciences, Imperial College London, London, UK
- Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kashyap A Patel
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK.
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Ng ACH, Chahine M, Scantlebury MH, Appendino JP. Channelopathies in epilepsy: an overview of clinical presentations, pathogenic mechanisms, and therapeutic insights. J Neurol 2024; 271:3063-3094. [PMID: 38607431 DOI: 10.1007/s00415-024-12352-x] [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: 03/17/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
Pathogenic variants in genes encoding ion channels are causal for various pediatric and adult neurological conditions. In particular, several epilepsy syndromes have been identified to be caused by specific channelopathies. These encompass a spectrum from self-limited epilepsies to developmental and epileptic encephalopathies spanning genetic and acquired causes. Several of these channelopathies have exquisite responses to specific antiseizure medications (ASMs), while others ASMs may prove ineffective or even worsen seizures. Some channelopathies demonstrate phenotypic pleiotropy and can cause other neurological conditions outside of epilepsy. This review aims to provide a comprehensive exploration of the pathophysiology of seizure generation, ion channels implicated in epilepsy, and several genetic epilepsies due to ion channel dysfunction. We outline the clinical presentation, pathogenesis, and the current state of basic science and clinical research for these channelopathies. In addition, we briefly look at potential precision therapy approaches emerging for these disorders.
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Affiliation(s)
- Andy Cheuk-Him Ng
- Clinical Neuroscience and Pediatric Neurology, Department of Pediatrics, Cumming School of Medicine, Alberta Children's Hospital, University of Calgary, 28 Oki Drive NW, Calgary, AB, T3B 6A8, Canada
- Division of Neurology, Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta and Stollery Children's Hospital, Edmonton, AB, Canada
| | - Mohamed Chahine
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- CERVO, Brain Research Centre, Quebec City, Canada
| | - Morris H Scantlebury
- Clinical Neuroscience and Pediatric Neurology, Department of Pediatrics, Cumming School of Medicine, Alberta Children's Hospital, University of Calgary, 28 Oki Drive NW, Calgary, AB, T3B 6A8, Canada
- Hotchkiss Brain Institute and Alberta Children's Hospital Research Institute, Calgary, Canada
| | - Juan P Appendino
- Clinical Neuroscience and Pediatric Neurology, Department of Pediatrics, Cumming School of Medicine, Alberta Children's Hospital, University of Calgary, 28 Oki Drive NW, Calgary, AB, T3B 6A8, Canada.
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João S, Quental R, Pinto J, Almeida C, Santos H, Dória S. Impact of copy number variants in epilepsy plus neurodevelopment disorders. Seizure 2024; 117:6-12. [PMID: 38277927 DOI: 10.1016/j.seizure.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
INTRODUCTION Epilepsy, a neurological disorder characterized by recurring unprovoked seizures due to excessive neuronal excitability, is primarily attributed to genetic factors, accounting for an estimated 70 % of cases. Array-comparative genomic hybridization (aCGH) is a crucial genetic test for detecting copy number variants (CNVs) associated with epilepsy. This study aimed to analyze a cohort of epilepsy patients with CNVs detected through aCGH to enhance our understanding of the genetic underpinnings of epilepsy. METHODS A retrospective cross-sectional study was conducted using the aCGH database from the Genetics Department of the Faculty of Medicine of the University of Porto, encompassing 146 patients diagnosed with epilepsy, epileptic encephalopathy, or seizures. Clinical data were collected, and aCGH was performed following established guidelines. CNVs were classified based on ACMG standards, and patients were categorized into four groups according to their clinical phenotype. RESULTS Among the 146 included patients, 94 (64 %) had at least one CNV, with 22 (15.1 %) classified as pathogenic or likely pathogenic. Chromosomes 1, 2, 16, and X were frequently implicated, with Xp22.33 being the most reported region (8 CNVs). The phenotype "Epilepsy and global developmental delay/intellectual disability" showed the highest prevalence of clinically relevant CNVs. Various CNVs were identified across different groups, suggesting potential roles in epilepsy. CONCLUSIONS This study highlights the significance of aCGH in unraveling the genetic basis of epilepsy and tailoring treatment strategies. It contributes valuable insights to the expanding knowledge in the field, emphasizing the need for research to elucidate the diverse genetic causes of epilepsy.
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Affiliation(s)
- Sofia João
- Department of Pathology - Genetics, Faculty of Medicine, University of Porto, Portugal.
| | - Rita Quental
- Medical Genetics Service, Centro Hospitalar Universitário de São João - CHUSJ, Porto, Portugal.
| | - Joel Pinto
- Department of Pathology - Genetics, Faculty of Medicine, University of Porto, Portugal; I3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
| | - Carolina Almeida
- Department of Pathology - Genetics, Faculty of Medicine, University of Porto, Portugal; I3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
| | - Helena Santos
- Child and Adolescent Neuroscience Unit, Centro Hospitalar Vila Nova de Gaia/Espinho - CHNVG, Vila Nova de Gaia, Portugal.
| | - Sofia Dória
- Department of Pathology - Genetics, Faculty of Medicine, University of Porto, Portugal; I3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
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Zhang MW, Liang XY, Wang J, Gao LD, Liao HJ, He YH, Yi YH, He N, Liao WP. Epilepsy-associated genes: an update. Seizure 2024; 116:4-13. [PMID: 37777370 DOI: 10.1016/j.seizure.2023.09.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/31/2023] [Accepted: 09/23/2023] [Indexed: 10/02/2023] Open
Abstract
PURPOSE To provide an updated list of epilepsy-associated genes based on clinical-genetic evidence. METHODS Epilepsy-associated genes were systematically searched and cross-checked from the OMIM, HGMD, and PubMed databases up to July 2023. To facilitate the reference for the epilepsy-associated genes that are potentially common in clinical practice, the epilepsy-associated genes were ranked by the mutation number in the HGMD database and by case number in the China Epilepsy Gene 1.0 project, which targeted common epilepsy. RESULTS Based on the OMIM database, 1506 genes were identified to be associated with epilepsy and were classified into three categories according to their potential association with epilepsy or other abnormal phenotypes, including 168 epilepsy genes that were associated with epilepsies as pure or core symptoms, 364 genes that were associated with neurodevelopmental disorders as the main symptom and epilepsy, and 974 epilepsy-related genes that were associated with gross physical/systemic abnormalities accompanied by epilepsy/seizures. Among the epilepsy genes, 115 genes (68.5%) were associated with epileptic encephalopathy. After cross-checking with the HGMD and PubMed databases, an additional 1440 genes were listed as potential epilepsy-associated genes, of which 278 genes have been repeatedly identified variants in patients with epilepsy. The top 100 frequently reported/identified epilepsy-associated genes from the HGMD database and the China Epilepsy Gene 1.0 project were listed, among which 40 genes were identical in both sources. SIGNIFICANCE Recognition of epilepsy-associated genes will facilitate genetic screening strategies and be helpful for precise molecular diagnosis and treatment of epilepsy in clinical practice.
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Affiliation(s)
- Meng-Wen Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Xiao-Yu Liang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Jie Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Liang-Di Gao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Han-Jun Liao
- University of South China, Hengyang, 421001, China
| | - Yun-Hua He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Yong-Hong Yi
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
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Spurgeon AL, Keaveney SF, Ng YT. Refractory Jeavons Syndrome from Birth Symptomatic to PLCB1 Mutation. Child Neurol Open 2023; 10:2329048X231183524. [PMID: 37441061 PMCID: PMC10334019 DOI: 10.1177/2329048x231183524] [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: 03/25/2023] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 07/15/2023] Open
Abstract
Jeavons syndrome is a common, often misdiagnosed or overlooked epileptic syndrome presenting with a triad of eyelid myoclonia with or without absence seizures, eye closure-induced EEG paroxysms, and photosensitivity. We present a seven-year-old female who presented with eyelid myoclonia evident since birth with absence seizures and migraines with associated photosensitivity. An EEG with photic stimulation confirmed the diagnosis of Jeavons syndrome. Genetic testing showed a heterozygous mutation in the PLCB1 gene which has been linked to early onset epilepsies and encephalopathic epilepsies. This mutation and her clinical presentation identifies another etiology of Jeavons syndrome and confirms it can begin from birth. Its presence highlights the importance of genetic testing in epileptic patients to better understand the links between genetics and epilepsy syndromes so appropriate treatment can be initiated.
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Affiliation(s)
| | | | - Yu-Tze Ng
- Department of Pediatric Neurology, University of Missouri School of Medicine,
Columbia, MO, USA
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Beltrán-Corbellini Á, Aledo-Serrano Á, Møller RS, Pérez-Palma E, García-Morales I, Toledano R, Gil-Nagel A. Epilepsy Genetics and Precision Medicine in Adults: A New Landscape for Developmental and Epileptic Encephalopathies. Front Neurol 2022; 13:777115. [PMID: 35250806 PMCID: PMC8891166 DOI: 10.3389/fneur.2022.777115] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/27/2022] [Indexed: 12/14/2022] Open
Abstract
This review aims to provide an updated perspective of epilepsy genetics and precision medicine in adult patients, with special focus on developmental and epileptic encephalopathies (DEEs), covering relevant and controversial issues, such as defining candidates for genetic testing, which genetic tests to request and how to interpret them. A literature review was conducted, including findings in the discussion and recommendations. DEEs are wide and phenotypically heterogeneous electroclinical syndromes. They generally have a pediatric presentation, but patients frequently reach adulthood still undiagnosed. Identifying the etiology is essential, because there lies the key for precision medicine. Phenotypes modify according to age, and although deep phenotyping has allowed to outline certain entities, genotype-phenotype correlations are still poor, commonly leading to long-lasting diagnostic odysseys and ineffective therapies. Recent adult series show that the target patients to be identified for genetic testing are those with epilepsy and different risk factors. The clinician should take active part in the assessment of the pathogenicity of the variants detected, especially concerning variants of uncertain significance. An accurate diagnosis implies precision medicine, meaning genetic counseling, prognosis, possible future therapies, and a reduction of iatrogeny. Up to date, there are a few tens of gene mutations with additional concrete treatments, including those with restrictive/substitutive therapies, those with therapies modifying signaling pathways, and channelopathies, that are worth to be assessed in adults. Further research is needed regarding phenotyping of adult syndromes, early diagnosis, and the development of targeted therapies.
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Affiliation(s)
| | - Ángel Aledo-Serrano
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid, Spain
- *Correspondence: Ángel Aledo-Serrano
| | - Rikke S. Møller
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
| | - Eduardo Pérez-Palma
- Universidad del Desarrollo, Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Santiago, Chile
| | - Irene García-Morales
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid, Spain
- Epilepsy Unit, Neurology Department, Clínico San Carlos University Hospital, Madrid, Spain
| | - Rafael Toledano
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid, Spain
- Epilepsy Unit, Neurology Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - Antonio Gil-Nagel
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid, Spain
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Involvement of Rare Mutations of SCN9A, DPP4, ABCA13, and SYT14 in Schizophrenia and Bipolar Disorder. Int J Mol Sci 2021; 22:ijms222413189. [PMID: 34947986 PMCID: PMC8709054 DOI: 10.3390/ijms222413189] [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: 11/19/2021] [Revised: 12/05/2021] [Accepted: 12/05/2021] [Indexed: 02/07/2023] Open
Abstract
Rare mutations associated with schizophrenia (SZ) and bipolar disorder (BD) usually have high clinical penetrance; however, they are highly heterogeneous and personalized. Identifying rare mutations is instrumental in making the molecular diagnosis, understanding the pathogenesis, and providing genetic counseling for the affected individuals and families. We conducted whole-genome sequencing analysis in two multiplex families with the dominant inheritance of SZ and BD. We detected a G327E mutation of SCN9A and an A654V mutation of DPP4 cosegregating with SZ and BD in one three-generation multiplex family. We also identified three mutations cosegregating with SZ and BD in another two-generation multiplex family, including L711S of SCN9A, M4554I of ABCA13, and P159L of SYT14. These five missense mutations were rare and deleterious. Mutations of SCN9A have initially been reported to cause congenital insensitivity to pain and neuropathic pain syndromes. Further studies showed that rare mutations of SCN9A were associated with seizure and autism spectrum disorders. Our findings suggest that SZ and BD might also be part of the clinical phenotype spectra of SCN9A mutations. Our study also indicates the oligogenic involvement in SZ and BD and supports the multiple-hit model of SZ and BD.
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Brunklaus A. No evidence that SCN9A variants are associated with epilepsy. Seizure 2021; 91:172-173. [PMID: 34171626 DOI: 10.1016/j.seizure.2021.05.026] [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: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- A Brunklaus
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, United Kingdom; Institute of Health and Wellbeing, University of Glasgow, Glasgow, United Kingdom.
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