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Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024:10.1038/s41576-024-00715-z. [PMID: 38605218 DOI: 10.1038/s41576-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.
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Affiliation(s)
- Sarah M Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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2
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Lecoquierre F, Cassinari K, Drouot N, May A, Fourneaux S, Charbonnier F, Derambure C, Coutant S, Saugier-Veber P, Hoischen A, Charbonnier C, Nicolas G. Assessment of parental mosaicism rates in neurodevelopmental disorders caused by apparent de novo pathogenic variants using deep sequencing. Sci Rep 2024; 14:5289. [PMID: 38438430 PMCID: PMC10912112 DOI: 10.1038/s41598-024-53358-9] [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: 11/28/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
While de novo variants (DNV) are overall at low risk of recurrence in subsequent pregnancies, a subset is at high risk due to parental mosaicism. Accurately identifying cases of parental mosaicism is therefore important for genetic counseling in clinical care. Some studies have investigated the rate of parental mosaics, but most were either limited by the sensitivity of the techniques (i.e. exome or genome sequencing), or focused on specific types of disease such as epileptic syndromes. This study aimed to determine the proportion of parental mosaicism among the DNV causing neurodevelopmental disorders (NDDs) in a series not enriched in epilepsy syndromes. We collected 189 patients with NDD-associated DNV. We applied a smMIP enrichment method and sequenced parental blood DNA samples to an average depth of 7000x. Power simulation indicated that mosaicism with an allelic fraction of 0.5% would have been detected for 87% of positions with 90% power. We observed seven parental mosaic variants (3.7% of families), of which four (2.1% of families) had an allelic fraction of less than 1%. In total, our study identifies a relatively low proportion of parental mosaicism in NDD-associated DNVs and raises the question of a biological mechanism behind the higher rates of parental mosaicism detected in other studies, particularly those focusing on epileptic syndromes.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France.
- Centre de Ressources Biologiques institutionnel du CHU de Rouen - Biothèque filière génétique, Rouen, France.
| | - Kévin Cassinari
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Angèle May
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Francoise Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Celine Derambure
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Camille Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
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Zeng B, Zhang H, Lu Q, Fu Q, Yan Y, Lu W, Ma P, Feng C, Qin J, Luo L, Yang B, Zou Y, Liu Y. Identification of five novel SCN1A variants. Front Behav Neurosci 2023; 17:1272748. [PMID: 38025388 PMCID: PMC10663289 DOI: 10.3389/fnbeh.2023.1272748] [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: 08/04/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Background Epilepsy is characterized by recurrent unprovoked seizures. Mutations in the voltage-gated sodium channel alpha subunit 1 (SCN1A) gene are the main monogenic cause of epilepsy. Type and location of variants make a huge difference in the severity of SCN1A disorder, ranging from the mild phenotype (genetic epilepsy with febrile seizures plus, GEFS+) to the severe phenotype (developmental and epileptic encephalopathies, DEEs). Dravet Syndrome (DS) is an infantile-onset DEE, characterized by drug-resistant epilepsy and temperature sensitivity or febrile seizures. Genetic test results reveal SCN1A variants are positive in 80% DS patients and DS is mainly caused by de novo variants. Methods Trio-whole exome sequencing (WES) was used to detect variants which were associated with clinical phenotype of five probands with epilepsy or twitching. Then, Sanger sequencing was performed to validate the five novel SCN1A variants and segregation analysis. After analyzing the location of five SCN1A variants, the pathogenic potential was assessed. Results In this study, we identified five novel SCN1A variants (c.4224G > C, c.3744_3752del, c.209del, c.5727_5734delTTTAAAACinsCTTAAAAAG and c.5776delT) as the causative variants. In the five novel SCN1A variants, four were de novo and the remaining one was inherited. All novel variants would be classified as "pathogenic" or "likely pathogenic." Conclusion The five novel SCN1A variants will enrich the SCN1A mutations database and provide the corresponding reference data for the further genetic counseling.
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Affiliation(s)
- Baitao Zeng
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Haoyi Zhang
- School of Public Health, Nanchang University, Nanchang, China
| | - Qing Lu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Qingzi Fu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yang Yan
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Wan Lu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Pengpeng Ma
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Chuanxin Feng
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Jiawei Qin
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Laipeng Luo
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Bicheng Yang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yongyi Zou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2023:10.1007/s12264-023-01124-8. [PMID: 37898991 DOI: 10.1007/s12264-023-01124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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Lee M, Lui ACY, Chan JCK, Doong PHL, Kwong AKY, Mak CCY, Li RHW, Kan ASY, Chung BHY. Revealing parental mosaicism: the hidden answer to the recurrence of apparent de novo variants. Hum Genomics 2023; 17:91. [PMID: 37798624 PMCID: PMC10557286 DOI: 10.1186/s40246-023-00535-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Mosaicism refers to the presence of two or more populations of genetically distinct cells within an individual, all of which originate from a single zygote. Previous literature estimated the percentage of parental mosaicism ranged from 0.33 to 25.9%. In this study, parents whose children had previously been diagnosed with developmental disorders with an apparent de novo variant were recruited. Peripheral blood, buccal and semen samples were collected from these parents if available for the detection of potential parental mosaicism using droplet digital PCR, complemented with the method of blocker displacement amplification. Among the 20 families being analyzed, we report four families with parental mosaicism (4/20, 20%). Two families have maternal gonosomal mosaicism (EYA1 and EBF3) and one family has paternal gonadal mosaicism (CHD7) with a pathogenic/ likely pathogenic variant. One family has a paternal gonosomal mosaicism with a variant of uncertain significance (FLNC) with high clinical relevance. The detectable variant allele frequency in our cohort ranged from 8.7-35.9%, limit of detection 0.08-0.16% based on our in-house EBF3 assay. Detecting parental mosaicism not only informs family with a more accurate recurrence risk, but also facilitates medical teams to create appropriate plans for pregnancy and delivery, offering the most suitable care.
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Affiliation(s)
- Mianne Lee
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Adrian C Y Lui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Joshua C K Chan
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Anna K Y Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Raymond H W Li
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Sai Wan Ho, Hong Kong SAR, China
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China.
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Ngau Tau Kok, Hong Kong SAR, China.
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Li X, Huang S, Wang G, Kang D, Han M, Wu X, Yang J, Zheng Q, Zhao C, Yuan Y, Dai P. Quantitative assessment of low-level parental mosaicism of SNVs and CNVs in Waardenburg syndrome. Hum Genet 2023; 142:419-430. [PMID: 36576601 DOI: 10.1007/s00439-022-02517-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022]
Abstract
Waardenburg syndrome (WS) is a rare inherited autosomal dominant disorder caused by SOX10, PAX3, MITF, EDNRB, EDN3, and SNAI2. A large burden of pathogenic de novo variants is present in patients with WS, which may be derived from parental mosaicism. Previously, we retrospectively analyzed 90 WS probands with family information. And the frequency of de novo events and parental mosaicism was preliminary investigated in our previous study. In this study, we further explored the occurrence of low-level parental mosaicism in 33 WS families with de novo variants and introduced our procedure of quantifying low-level mosaicism. Mosaic single nucleotide polymorphisms (SNPs) were validated by amplicon-based next-generation sequencing (NGS); copy-number variants (CNVs) were validated by droplet-digital polymerase chain reaction (ddPCR). Molecular validation of low-level mosaicism of WS-causing variants was performed in four families (12.1%, 4/33). These four mosaic variants, comprising three SNVs and one CNV, were identified in SOX10. The rate of parental mosaicism was 25% (4/16) in WS families with de novo SOX10 variants. The lowest allele ratio of a mosaic variant was 2.0% in parental saliva. These de novo WS cases were explained by parental mosaicism conferring an elevated recurrence risk in subsequent pregnancies of parents. Considering its importance in genetic counseling, low-level parental mosaicism should be systematically investigated by personalized sensitive testing. Amplicon-based NGS and ddPCR are recommended to detect and precisely quantify the mosaicism for SNPs and CNVs.
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Affiliation(s)
- Xiaohong Li
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China.,Department of Otorhinolaryngology Head and Neck Surgery, Key Laboratory for Pediatric Diseases of Otolaryngology-Head and Neck Surgery, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China
| | - Guojian Wang
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China
| | - Dongyang Kang
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China
| | - Mingyu Han
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China
| | - Xiedong Wu
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China
| | - Jinyuan Yang
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China
| | - Qiuchen Zheng
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China
| | - Chaoyue Zhao
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China.
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, The Sixth Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, #28 Fuxing Road, Beijing, 100853, China.
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D'Gama AM, Poduri A. Brain somatic mosaicism in epilepsy: Bringing results Back to the clinic. Neurobiol Dis 2023; 181:106104. [PMID: 36972791 DOI: 10.1016/j.nbd.2023.106104] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/28/2023] Open
Abstract
Over the past decade, there has been tremendous progress in understanding brain somatic mosaicism in epilepsy in the research setting. Access to resected brain tissue samples from patients with medically refractory epilepsy undergoing epilepsy surgery has been key to making these discoveries. In this review, we discuss the gap between making discoveries in the research setting and bringing results back to the clinical setting. Current clinical genetic testing mainly uses clinically accessible tissue samples, like blood and saliva, and can detect inherited and de novo germline variants and potentially non-brain-limited mosaic variants that have resulted from post-zygotic mutation (also called "somatic mutations"). Methods developed in the research setting to detect brain-limited mosaic variants using brain tissue samples need to be further translated and validated in the clinical setting, which will allow post-resection brain tissue genetic diagnoses. However, obtaining a genetic diagnosis after surgery for refractory focal epilepsy, when brain tissue samples are available, is arguably "too late" to guide precision management. Emerging methods using cerebrospinal fluid (CSF) and subdural electroencephalogram (SEEG) depth electrodes hold promise for establishing genetic diagnoses pre-resection without the need for actual brain tissue. In parallel, development of curation rules for interpreting the pathogenicity of mosaic variants, which have unique considerations compared to germline variants, will assist clinically accredited laboratories and epilepsy geneticists in making genetic diagnoses. Returning results of brain-limited mosaic variants to patients and their families will end their diagnostic odyssey and advance epilepsy precision management.
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The emergence of genotypic divergence and future precision medicine applications. HANDBOOK OF CLINICAL NEUROLOGY 2023; 192:87-99. [PMID: 36796950 DOI: 10.1016/b978-0-323-85538-9.00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Genotypic divergence is a term adapted from population genetics and intimately linked to evolution. We use divergence here to emphasize the differences that set individuals apart in any cohort. The history of genetics is filled with descriptions of genotypic differences, but causal inference of interindividual biological variation has been scarce. We suggest that the practice of precision medicine requires a divergent approach, an approach dependent on the causal interpretation of previous convergent (and preliminary) knowledge in the field. This knowledge has relied on convergent descriptive syndromology (lumping), which has overemphasized a reductionistic gene determinism on the quest of seeking associations without causal understanding. Regulatory variants with small effect and somatic mutations are some of the modifying factors that lead to incomplete penetrance and intrafamilial variable expressivity often observed in apparently monogenic clinical disorders. A truly divergent approach to precision medicine requires splitting, that is, the consideration of different layers of genetic phenomena that interact causally in a nonlinear fashion. This chapter reviews convergences and divergences in genetics and genomics, aiming to discuss what can be causally understood to approximate the as-yet utopian lands of Precision Medicine for patients with neurodegenerative disorders.
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9
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Chen J, Chen Y, Yang Y, Niu X, Zhang J, Zeng Q, Liu A, Xu X, Yang X, Li S, Yang X, Wang Y, Zhang Y. Detecting genomic mosaicism in "de novo" genetic epilepsy by amplicon-based deep sequencing. J Hum Genet 2023; 68:73-80. [PMID: 36482122 DOI: 10.1038/s10038-022-01103-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
AIM To investigate the occurrence of mosaicism in epilepsy probands and their parents using amplicon-based deep sequencing (ADS). METHODS Patients were recruited from the outpatient of Peking University First Hospital. Two hundred and sixty-four probands with pathogenic variants tested by next-generation sequencing (NGS) were enrolled. RESULTS Mosaic variants were detected in seventeen disease-associated genes from 20 probands, 5 paternal, and 6 maternal parents. The frequency of mosaicism was 11.74% (31/264). Mosaicism in 11 genes was identified from 20 probands with the mutant allelic fractions (MAFs) of 12.95-38.00% in autosomal dominant genes. Five paternal mosaicisms were identified in genes with a MAF of 6.30-20.99%, and six maternal mosaic individuals with a MAF of 2.07-21.90%. Only four mosaic parents had milder seizure history. The affected sibling had the same phenotype consistent with that of the proband, who inherited the variant of SLC1A2 or STXBP1 from their unaffected mosaic mothers, respectively. INTERPRETATION Mosaic phenomenon is not rare in families with epilepsy. Phenotypes of mosaic parents were milder or normal. Mosaicism detection is helpful to identify the mutation origin and it provides a theoretical basis for prenatal diagnosis of family reproduction. ADS is a reliable way of mosaicism detection for clinical application.
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Affiliation(s)
- Jiaoyang Chen
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Yi Chen
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Ying Yang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Xueyang Niu
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Jing Zhang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Qi Zeng
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Aijie Liu
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Xiaojing Xu
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Xiaoxu Yang
- Center for Bioinformatics, Peking University, Beijing, 100871, China
| | - Shupin Li
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Xiaoling Yang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Yi Wang
- Department of Neurology, National Epilepsy Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Yuehua Zhang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China.
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10
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Mavashov A, Brusel M, Liu J, Woytowicz V, Bae H, Chen YH, Dani VS, Cardenal-Muñoz E, Spinosa V, Aibar JÁ, Rubinstein M. Heat-induced seizures, premature mortality, and hyperactivity in a novel Scn1a nonsense model for Dravet syndrome. Front Cell Neurosci 2023; 17:1149391. [PMID: 37206664 PMCID: PMC10191256 DOI: 10.3389/fncel.2023.1149391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/05/2023] [Indexed: 05/21/2023] Open
Abstract
Dravet syndrome (Dravet) is a severe congenital developmental genetic epilepsy caused by de novo mutations in the SCN1A gene. Nonsense mutations are found in ∼20% of the patients, and the R613X mutation was identified in multiple patients. Here we characterized the epileptic and non-epileptic phenotypes of a novel preclinical Dravet mouse model harboring the R613X nonsense Scn1a mutation. Scn1aWT/R613X mice, on a mixed C57BL/6J:129S1/SvImJ background, exhibited spontaneous seizures, susceptibility to heat-induced seizures, and premature mortality, recapitulating the core epileptic phenotypes of Dravet. In addition, these mice, available as an open-access model, demonstrated increased locomotor activity in the open-field test, modeling some non-epileptic Dravet-associated phenotypes. Conversely, Scn1aWT/R613X mice, on the pure 129S1/SvImJ background, had a normal life span and were easy to breed. Homozygous Scn1aR613X/R613X mice (pure 129S1/SvImJ background) died before P16. Our molecular analyses of hippocampal and cortical expression demonstrated that the premature stop codon induced by the R613X mutation reduced Scn1a mRNA and NaV1.1 protein levels to ∼50% in heterozygous Scn1aWT/R613X mice (on either genetic background), with marginal expression in homozygous Scn1aR613X/R613X mice. Together, we introduce a novel Dravet model carrying the R613X Scn1a nonsense mutation that can be used to study the molecular and neuronal basis of Dravet, as well as the development of new therapies associated with SCN1A nonsense mutations in Dravet.
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Affiliation(s)
- Anat Mavashov
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Goldschleger Eye Research Institute, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marina Brusel
- Goldschleger Eye Research Institute, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jiaxing Liu
- Tevard Biosciences, Cambridge, MA, United States
| | | | - Haneui Bae
- Tevard Biosciences, Cambridge, MA, United States
| | | | | | | | | | | | - Moran Rubinstein
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Goldschleger Eye Research Institute, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- *Correspondence: Moran Rubinstein,
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11
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Rojnueangnit K, Anthanont P, Khetkham T, Puttamanee S, Ittiwut C. Genetic diagnosis for adult patients at a genetic clinic. Cold Spring Harb Mol Case Stud 2022; 8:a006235. [PMID: 36265913 PMCID: PMC9808555 DOI: 10.1101/mcs.a006235] [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] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/04/2022] [Indexed: 01/31/2023] Open
Abstract
Clinical utility of genetic testing has rapidly increased in the past decade to identify the definitive diagnosis, etiology, and specific management. The majority of patients receiving testing are children. There are several barriers for genetic tests in adult patients; barriers may arise from either patients or clinicians. Our study aims to realize the detection rate and the benefits of genetic tests in adults. We conducted a prospective study of 10 adult patients who were referred to a genetic clinic. Exome sequencing (ES) was pursued in all cases, and chromosomal microarray (CMA) was performed for six cases. Our result is impressive; six cases (60%) received likely pathogenic and pathogenic variants. Four definitive diagnosis cases had known pathogenic variants in KCNJ2, TGFBR1, SCN1A, and FBN1, whereas another two cases revealed novel likely pathogenic and pathogenic variants in GNB1 and DNAH9. Our study demonstrates the success in genetic diagnosis in adult patients: four cases with definitive, two cases with possible, and one case with partial diagnosis. The advantage of diagnosis is beyond obtaining the diagnosis itself, but also relieving any doubt for the patient regarding any previous questionable diagnosis, guide for management, and recurrence risk in their children or family members. Therefore, this supports the value of genetic testing in adult patients.
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Affiliation(s)
- Kitiwan Rojnueangnit
- Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathumthani, 12120 Thailand
| | - Pimjai Anthanont
- Department of Medicine, Faculty of Medicine, Thammasat University, Pathumthani, 12120 Thailand
| | - Thanitchet Khetkham
- Division of Forensic Medicine, Thammasat University Hospital, 12120 Thailand
| | - Sukita Puttamanee
- Faculty of Medicine, Thammasat University, Pathumthani, 12120 Thailand
| | - Chupong Ittiwut
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330 Thailand
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12
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Chen Y, Yang X, Chen J, Yang X, Yang Y, Liu A, Zhang X, Wu W, Sun D, Yang Z, Jiang Y, Zhang Y. PCDH19-related epilepsy in mosaic males: The phenotypic implication of genotype and variant allele frequency. Front Neurol 2022; 13:1041509. [PMID: 36408521 PMCID: PMC9669318 DOI: 10.3389/fneur.2022.1041509] [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: 09/11/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2023] Open
Abstract
OBJECTIVE To analyze the genotypes and phenotypes of mosaic male patients with PCDH19-related epilepsy (PCDH19-RE) and explore the correlation between genotype, variant allele frequency (VAF), and phenotypic severity. METHODS Clinical data and peripheral blood samples of 11 male mosaic patients were collected and analyzed in our study. The VAF of the PCDH19 gene from peripheral blood was quantified using amplicon-based deep sequencing. Additional 20 mosaic male patients with PCDH19-RE were collected from the published literature, with 10 patients whose VAFs of the PCDH19 gene were available for analytic purposes. RESULTS In our cohort of 11 patients, 10 variants were identified, and four were novel. The VAF of the PCDH19 gene from peripheral blood ranged from 27 to 90%. The median seizure onset age was 6 months (range: 4-9 months). Clinical manifestations included cluster seizures (100%), fever sensitivity (73%), focal seizures (91%), developmental delay/intellectual disability (DD/ID, 82%), and autistic features (45%). Thirty-one mosaic male patients collected from our cohort and the literature developed seizures mostly (87%) within one year of age. Variant types included missense variants (42%), truncating variants (52%), splice variants (3%), and whole PCDH19 deletion (3%). Among 21 patients with a definite VAF from our cohort and the literature, nine had a low VAF ( ≤ 50%) and 12 had a high VAF (> 50%). Seventy-five percent of variants from the high VAF group were missense, whereas 89% of those from the low VAF group were truncations. The median seizure onset age was 6 months in the low VAF group and 9 months in the high VAF group (p = 0.018). Forty-four percent (4/9) of patients from the low VAF group achieved seizure-free for ≥1 year, whereas none of the 12 patients from the high VAF group did (p = 0.021). DD/ID was present in 83% (10/12) of the high VAF group and 56% (5/9) of the low VAF group (p = 0.331). CONCLUSION The predominant variant types were truncating and missense variants. Missense variants tended to have higher VAFs. Patients with a high VAF were more likely to have a more severe epileptic phenotype. Our findings shed light on the phenotypic implications of VAF in mosaic males with PCDH19-RE.
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Affiliation(s)
- Yi Chen
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jiaoyang Chen
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ying Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Aijie Liu
- Department of Pediatric Neurology, Capital Institute of Pediatrics, Beijing, China
| | - Xiaoli Zhang
- Department of Pediatrics, The Third Affiliated Hospital of Zheng Zhou University, Zhengzhou, China
| | - Wenjuan Wu
- Department of Neurology, Hebei Children's Hospital, Shijiazhuang, China
| | - Dan Sun
- Department of Neurology, Wuhan Children's Hospital, Wuhan, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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13
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He Z, Li Y, Zhao X, Li B. Dravet Syndrome: Advances in Etiology, Clinical Presentation, and Treatment. Epilepsy Res 2022; 188:107041. [DOI: 10.1016/j.eplepsyres.2022.107041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/08/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022]
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14
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Phenotypic and Genotypic Spectrum of Early-Onset Developmental and Epileptic Encephalopathies-Data from a Romanian Cohort. Genes (Basel) 2022; 13:genes13071253. [PMID: 35886038 PMCID: PMC9322987 DOI: 10.3390/genes13071253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Early-onset developmental epileptic encephalopathy (DEE) refers to an age-specific, diverse group of epilepsy syndromes with electroclinical anomalies that are associated with severe cognitive, behavioral, and developmental impairments. Genetic DEEs have heterogeneous etiologies. This study includes 36 Romanian patients referred to the Regional Centre for Medical Genetics Dolj for genetic testing between 2017 and 2020. The patients had been admitted to and clinically evaluated at Doctor Victor Gomoiu Children’s Hospital and Prof. Dr. Alexandru Obregia Psychiatry Hospital in Bucharest. Panel testing was performed using the Illumina® TruSight™ One “clinical exome” (4811 genes), and the analysis focused on the known genes reported in DEEs and clinical concordance. The overall diagnostic rate was 25% (9/36 cases). Seven cases were diagnosed with Dravet syndrome (likely pathogenic/pathogenic variants in SCN1A) and two with Genetic Epilepsy with Febrile Seizures Plus (SCN1B). For the diagnosed patients, seizure onset was <1 year, and the seizure type was generalized tonic-clonic. Four additional plausible variants of unknown significance in SCN2A, SCN9A, and SLC2A1 correlated with the reported phenotype. Overall, we are reporting seven novel variants. Comprehensive clinical phenotyping is crucial for variant interpretation. Genetic assessment of patients with severe early-onset DEE can be a powerful diagnostic tool for clinicians, with implications for the management and counseling of the patients and their families.
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15
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Sharkov A, Sparber P, Stepanova A, Pyankov D, Korostelev S, Skoblov M. Case Report: Phenotype-Driven Diagnosis of Atypical Dravet-Like Syndrome Caused by a Novel Splicing Variant in the SCN2A Gene. Front Genet 2022; 13:888481. [PMID: 35711923 PMCID: PMC9194094 DOI: 10.3389/fgene.2022.888481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/19/2022] [Indexed: 01/18/2023] Open
Abstract
Febrile-associated epileptic encephalopathy is a large genetically heterogeneous group that is associated with pathogenic variants in SCN1A, PCDH19, SCN2A, SCN8A, and other genes. The disease onset ranges from neonatal or early-onset epileptic encephalopathy to late-onset epilepsy after 18 months. Some etiology-specific epileptic encephalopathies have target therapy which can serve as a clue for the correct genetic diagnosis. We present genetic, clinical, electroencephalographic, and behavioral features of a 4-year-old girl with epileptic encephalopathy related to a de novo intronic variant in the SCN2A gene. Initial NGS analysis revealed a frameshift variant in the KDM6A gene and a previously reported missense variant in SCN1A. Due to lack of typical clinical signs of Kabuki syndrome, we performed X-chromosome inactivation that revealed nearly complete skewed inactivation. Segregation analysis showed that the SCN1A variant was inherited from a healthy father. The proband had resistance to multiple antiseizure medications but responded well to sodium channel inhibitor Carbamazepine. Reanalysis of NGS data by a neurogeneticist revealed a previously uncharacterized heterozygous variant c.1035-7A>G in the SCN2A gene. Minigene assay showed that the c.1035-7A>G variant activates a cryptic intronic acceptor site which leads to 6-nucleotide extension of exon 9 (NP_066287.2:p.(Gly345_Gln346insTyrSer). SCN2A encephalopathy is a recognizable severe phenotype. Its electro-clinical and treatment response features can serve as a hallmark. In such a patient, reanalysis of genetic data is strongly recommended in case of negative or conflicting results of DNA analysis.
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Affiliation(s)
- Artem Sharkov
- Genomed Ltd., Moscow, Russia.,Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Peter Sparber
- Research Centre for Medical Genetics, Moscow, Russia
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16
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Genetics and gene therapy in Dravet syndrome. Epilepsy Behav 2022; 131:108043. [PMID: 34053869 DOI: 10.1016/j.yebeh.2021.108043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 05/02/2021] [Accepted: 05/02/2021] [Indexed: 12/17/2022]
Abstract
Dravet syndrome is a well-established electro-clinical condition first described in 1978. A main genetic cause was identified with the discovery of a loss-of-function SCN1A variant in 2001. Mechanisms underlying the phenotypic variations have subsequently been a main topic of research. Various genetic modifiers of clinical severities have been elucidated through many rigorous studies on genotype-phenotype correlations and the recent advances in next generation sequencing technology. Furthermore, a deeper understanding of the regulation of gene expression and remarkable progress on genome-editing technology using the CRISPR-Cas9 system provide significant opportunities to overcome hurdles of gene therapy, such as enhancing NaV1.1 expression. This article reviews the current understanding of genetic pathology and the status of research toward the development of gene therapy for Dravet syndrome. This article is part of the Special Issue "Severe Infantile Epilepsies".
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17
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Ma R, Duan Y, Zhang L, Qi X, Zhang L, Pan S, Gao L, Wang C, Wang Y. SCN1A-Related Epilepsy: Novel Mutations and Rare Phenotypes. Front Mol Neurosci 2022; 15:826183. [PMID: 35663268 PMCID: PMC9162153 DOI: 10.3389/fnmol.2022.826183] [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: 11/30/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesTo expand the genotypes and phenotypes of sodium voltage-gated channel alpha subunit 1 (SCN1A)-related epilepsy.MethodsWe retrospectively collected the clinical and genetic information of 22 epilepsy patients (10 males, 12 females; mean: 9.2 ± 3.9 years; 3.9–20.3 years) carrying 22 variants of SCN1A. SCN1A mutations were identified by next-generation sequencing.ResultsTwenty-two variants were identified, among which 12 have not yet been reported. The median age at seizure onset was 6 months. Sixteen patients were diagnosed with Dravet syndrome (DS), two with genetic epilepsy with febrile seizures plus [one evolved into benign epilepsy with centrotemporal spikes (BECTS)], one with focal epilepsy, one with atypical childhood epilepsy with centrotemporal spikes (ABECTS) and two with unclassified epilepsy. Fourteen patients showed a global developmental delay/intellectual disability (GDD/ID). Slow background activities were observed in one patient and epileptiform discharges were observed in 11 patients during the interictal phase.SignificanceThis study enriches the genotypes and phenotypes of SCN1A-related epilepsy. The clinical characteristics of patients with 12 previously unreported variants were described.
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18
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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19
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Frisk S, Wachtmeister A, Laurell T, Lindstrand A, Jäntti N, Malmgren H, Lagerstedt-Robinson K, Tesi B, Taylan F, Nordgren A. Detection of germline mosaicism in fathers of children with intellectual disability syndromes caused by de novo variants. Mol Genet Genomic Med 2022; 10:e1880. [PMID: 35118825 PMCID: PMC9000944 DOI: 10.1002/mgg3.1880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background De novo variants are a common cause to rare intellectual disability syndromes, associated with low recurrence risk. However, when such variants occur pre‐zygotically in parental germ cells, the recurrence risk might be higher. Still, the recurrence risk estimates are mainly based on empirical data and the prevalence of germline mosaicism is often unknown. Methods To establish the prevalence of mosaicism in parents of children with intellectual disability syndromes caused by de novo variants, we performed droplet digital PCR on DNA extracted from blood (43 trios), and sperm (31 fathers). Results We detected low‐level mosaicism in sperm‐derived DNA but not in blood in the father of a child with Kleefstra syndrome caused by an EHMT1 variant. Additionally, we found a higher level of paternal mosaicism in sperm compared to blood in the father of a child with Gillespie syndrome caused by an ITPR1 variant. Conclusion By employing droplet digital PCR, we detected paternal germline mosaicism in two intellectual disability syndromes. In both cases, the mosaicism level was higher in sperm than blood, indicating that analysis of blood alone may underestimate germline mosaicism. Therefore, sperm analysis can be clinically useful to establish the recurrence risk for parents and improve genetic counselling.
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Affiliation(s)
- Sofia Frisk
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Alexandra Wachtmeister
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Laurell
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Hand Surgery, Södersjukhuset, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Nina Jäntti
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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20
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Xu C, Yang C, Ye Q, Xu J, Tong L, Zhang Y, Shen H, Lu Z, Wang J, Lai E, Mao J, Jiang P. Mosaic PKHD1 in Polycystic Kidneys Caused Aberrant Protein Expression in the Mitochondria and Lysosomes. Front Med (Lausanne) 2022; 8:743150. [PMID: 34977057 PMCID: PMC8716551 DOI: 10.3389/fmed.2021.743150] [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: 07/17/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is a severe renal cystic disease caused mainly by the polycystic kidney and hepatic disease 1 (PKHD1). However, the genetic cause, pathologic features, and mechanism of action of ARPKD are not well known. Here, we identified a family with ARPKD. Two siblings harbored biallelic variants in PKHD1 (c.7205G>A, c.7973T>A). We determined that the "de novo" variant, c.7205G>A, arose from the mosaicism of the father and had a 7.4% level. Pathologic characterization, using biopsy analysis, was evidenced with predominant cystic dilation in proximal tubules, slight ectasia of collecting ducts, defective ciliogenesis, and impaired cell-cell junctions in renal tubules and collecting ducts. Exosome proteomics in the urine from patients with ARPKD were markedly different from those of controls, with the most significant alterations occurring in mitochondrial and lysosomal proteins. Expression of the proteins of OXPHOS was downregulated sharply, in parallel with upregulated expression of the proteins involved in glycolysis in patients with ARPKD. Several lysosomal proteins associated with renal lesions were more abundant in the exosome of the patient than in controls. Moreover, the lysosomal enzyme sulfamidase, which is produced by the SGSH gene, was abrupt uniquely in the exosome of the patient. Consistently, swollen mitochondria and abundant lysosomes were visualized in the mutant tubular epithelial cells of patients with mutant PKHD1. Collectively, these findings provide new insights on the pathophysiology of the polycystic kidney due to PKHD1 deficiency. PKHD1 mosaicism should be considered in genetic testing of ARPKD patients.
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Affiliation(s)
- Chengxian Xu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Chenxi Yang
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Qing Ye
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Jie Xu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Lingxiao Tong
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Yuchen Zhang
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Huijun Shen
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Zhihong Lu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Jingjing Wang
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Enyin Lai
- Department of Physiology, School of Basic Medical Sciences, and Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianhua Mao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorders, Hangzhou, China
| | - Pingping Jiang
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China.,Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorders, Hangzhou, China
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21
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Khamdiyeva O, Tileules Z, Baratzhanova G, Perfilyeva A, Djansugurova L. The study of sodium and potassium channel gene single-nucleotide variation significance in non-mechanical forms of epilepsy. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-020-00123-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Epilepsy is one of the most common and heterogeneous neurological diseases. The main clinical signs of the disease are repeated symptomatic or idiopathic epileptic seizures of both convulsive and non-convulsive nature that develop against a background of lost or preserved consciousness. The genetic component plays a large role in the etiology of idiopathic forms of epilepsy. The study of the molecular genetic basis of neurological disorders has led to a rapidly growing number of gene mutations known to be involved in hereditary ion channel dysfunction. The aim of this research was to evaluate the involvement of single-nucleotide variants that modify the function of genes (SCN1A, KCNT1, KCNTС1, and KCNQ2) encoding sodium and potassium ion channel polypeptides in the development of epilepsy.
Results
De novo mutations in the sodium channel gene SCN1A c.5347G>A (p. Ala1783Thr) were detected in two patients with Dravet syndrome, with a deletion in exon 26 found in one. Three de novo mutations in the potassium channel gene KCNT1 c.2800G>A (p. Ala934Thr), were observed in two patients with temporal lobe epilepsy (TLE) and one patient with residual encephalopathy. Moreover, a control cohort matched to the case cohort did not reveal any SNVs among conditionally healthy individuals, supporting the pathogenic significance of the studied SNVs.
Conclusion
Our results are supported by literature data showing that the sodium ion channel gene SCN1A c.5347G>A mutation may be involved in the pathogenesis of Dravet syndrome. We also note that the c.2800G>A mutation in the potassium channel gene KCNT1 can cause not only autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE) but also other forms of epilepsy. To treat pathogenetic mutations that accelerate the function of sodium and potassium ion channels, we recommend ion channel blockade drug therapy.
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22
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Jukkarwala A, Menon RN, Sunesh ER, Radhakrishnan A. Electroclinical Phenotype-Genotype Homogeneity in Drug-Resistant "Generalized" Tonic-Clonic Seizures of Early Childhood. Clin EEG Neurosci 2021; 52:371-375. [PMID: 32880473 DOI: 10.1177/1550059420953735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
PURPOSE Children with refractory focal to bilateral tonic-clonic seizures, despite normal high-resolution imaging, are often not subjected to genetic tests due to the costs involved and instead undergo multimodality presurgical evaluation targeted at delineating a focal onset. The objective of this study was to ascertain genotype-phenotype correlations in this group of patients. METHOD An online hospital database search was conducted for children who presented in 2019 with drug-resistant epilepsy dominated by nonlateralizing focal-onset/rapid generalized (bilateral) tonic-clonic seizures (GTCS), subjected to presurgical evaluation and subsequent genetic testing due to absence of a clear focus hypothesis. RESULTS Phenotypic homogeneity was apparent in 3 children who had onset in infancy with drug-resistant GTCS (predominantly unprovoked and occasionally fever provoked) and subsequent delayed development. 3-Tesla magnetic resonance imaging (MRI) scans were negative and video EEG documented a homogeneous pattern of multifocal and/or generalized epileptiform discharges with phenomenology favoring probable focal-onset/generalized-onset bilateral tonic-clonic seizures. All 3 tested positive for SCN1A gene variants (heterozygous missense substitution variants in 2 children, one of which was novel and a novel duplication in one that led to frameshift and premature truncation of the protein), suggestive of SCN1A-mediated epilepsy. This electroclinical profile constituted 3 out of 25 patients with SCN1A-epilepsy phenotypes at our center. CONCLUSIONS These cases suggest that children with early-onset drug-resistant "generalized" epilepsy are likely to have a genetic basis although the presentation may not be typical of Dravet syndrome. Hence, genetic testing for SCN1A variants is recommended in children with drug-resistant MRI negative focal-onset/generalized-onset bilateral tonic-clonic seizures before subjecting them to exhaustive presurgical workup and to guide appropriate treatment and prognostication.
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Affiliation(s)
- Anis Jukkarwala
- Geetanjali Medical College & Hospital, Udaipur, Rajasthan, India
| | - Ramshekhar N Menon
- Sree Chitra Tirunal Institute for Medical Sciences & Technology, Trivandrum, Kerala, India
| | - E R Sunesh
- Sree Chitra Tirunal Institute for Medical Sciences & Technology, Trivandrum, Kerala, India
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23
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Chmielewska JJ, Burkardt D, Granadillo JL, Slaugh R, Morgan S, Rotenberg J, Keren B, Mignot C, Escobar L, Turnpenny P, Zuteck M, Seaver LH, Ploski R, Dziembowska M, Wynshaw-Boris A, Adegbola A. PTPN4 germline variants result in aberrant neurodevelopment and growth. HGG ADVANCES 2021; 2:100033. [PMID: 34527963 PMCID: PMC8439436 DOI: 10.1016/j.xhgg.2021.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/31/2021] [Indexed: 11/29/2022] Open
Abstract
Protein-tyrosine phosphatases (PTPs) are pleomorphic regulators of eukaryotic cellular responses to extracellular signals that function by modulating the phosphotyrosine of specific proteins. A handful of PTPs have been implicated in germline and somatic human disease. Using exome sequencing, we identified missense and truncating variants in PTPN4 in six unrelated individuals with varying degrees of intellectual disability or developmental delay. The variants occurred de novo in all five subjects in whom segregation analysis was possible. Recurring features include postnatal growth deficiency or excess, seizures, and, less commonly, structural CNS, heart, or skeletal anomalies. PTPN4 is a widely expressed protein tyrosine phosphatase that regulates neuronal cell homeostasis by protecting neurons against apoptosis. We suggest that pathogenic variants in PTPN4 confer risk for growth and cognitive abnormalities in humans.
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Affiliation(s)
- Joanna J. Chmielewska
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
- Laboratory of Molecular Basis of Synaptic Plasticity, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Deepika Burkardt
- Center for Human Genetics and Department of Genetics and Genome Sciences, University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH, USA
| | - Jorge Luis Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Boris Keren
- Département de Génétique, APHP, Sorbonne Université, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Cyril Mignot
- Département de Génétique, APHP, Sorbonne Université, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Luis Escobar
- Medical Genetics and Neurodevelopmental Center, Peyton Manning Children’s Hospital, Indianapolis, IN, USA
| | - Peter Turnpenny
- University of Exeter Medical School and Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Melissa Zuteck
- Medical Genetics and Genomics, Spectrum Health/Helen Devos Children’s Hospital, Grand Rapids, MI, USA
| | - Laurie H. Seaver
- Medical Genetics and Genomics, Spectrum Health/Helen Devos Children’s Hospital, Grand Rapids, MI, USA
- Department of Pediatrics and Human Development, Michigan State College of Human Medicine, Grand Rapids, MI, USA
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Magdalena Dziembowska
- Laboratory of Molecular Basis of Synaptic Plasticity, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Anthony Wynshaw-Boris
- Center for Human Genetics and Department of Genetics and Genome Sciences, University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH, USA
| | - Abidemi Adegbola
- Center for Human Genetics and Department of Genetics and Genome Sciences, University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH, USA
- Department of Psychiatry, University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, OH, USA
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24
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Yu W, Smolen CE, Hill SF, Meisler MH. Spontaneous seizures and elevated seizure susceptibility in response to somatic mutation of sodium channel Scn8a in the mouse. Hum Mol Genet 2021; 30:902-907. [PMID: 33822038 PMCID: PMC8165645 DOI: 10.1093/hmg/ddab092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 02/05/2023] Open
Abstract
De novo mutations of neuronal sodium channels are responsible for ~5% of developmental and epileptic encephalopathies, but the role of somatic mutation of these genes in adult-onset epilepsy is not known. We evaluated the role of post-zygotic somatic mutation by adult activation of a conditional allele of the pathogenic variant Scn8aR1872W in the mouse. After activation of CAG-Cre-ER by tamoxifen, the mutant transcript was expressed throughout the brain at a level proportional to tamoxifen dose. The threshold for generation of spontaneous seizures was reached when the proportion of mutant transcript reached 8% of total Scn8a transcript, equivalent to expression of the epileptogenic variant in 16% of heterozygous neurons. Expression below this level did not result in spontaneous seizures, but did increase susceptibility to seizure induction by kainate or auditory stimulation. The relatively high threshold for spontaneous seizures indicates that somatic mutation of sodium channels is unlikely to contribute to the elevated incidence of epilepsy in the elderly population. However, somatic mutation could increase susceptibility to other seizure stimuli.
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Affiliation(s)
- Wenxi Yu
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Corrine E Smolen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Sophie F Hill
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109 USA
| | - Miriam H Meisler
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109 USA
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25
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Izumi T, Aihara Y, Kikuchi A, Kure S. Electroencephalographic findings and genetic characterization of two brothers with IQSEC2 pathogenic variant. Brain Dev 2021; 43:652-656. [PMID: 33494955 DOI: 10.1016/j.braindev.2020.12.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/19/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
Two brothers with an IQSEC2 pathogenic variant presented with early onset intellectual disability, intractable epileptic seizures, autism spectrum disorders, postnatal microcephalus and slowly progressive rigid-spasticity. Their epileptic seizures were characterized by intractability, early onset epileptic spasms, and then clusters of tonic/tonic-clonic seizures, exacerbated by valproate. Electroencephalography showed periodic discharges, including periodic high voltage slow complexes and burst-suppression activity. Whole exome sequencing, using DNA from peripheral blood of both brothers, identified a pathogenic variant, c.2776 C > T, p.(Arg 926*) in exon 9 of IQSEC2 (NM 001111125.3). Their parents and another brother did not have this variant, which may suggest that maternal gonadal mosaicism is the most likely mechanism.
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Affiliation(s)
- Tatsuro Izumi
- Department of Pediatrics and Child Neurology, Nanao National Hospital, Nanao, Ishikawa 9268531, Japan.
| | - Yu Aihara
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi 9808575, Japan
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi 9808575, Japan
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi 9808575, Japan
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26
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Fernández-Álvarez P, Codina-Sola M, Valenzuela I, Teixidó-Turá G, Cueto-González A, Paramonov I, Antolín M, López-Grondona F, Vendrell T, Evangelista A, García-Arumí E, Tizzano EF. A systematic study and literature review of parental somatic mosaicism of FBN1 pathogenic variants in Marfan syndrome. J Med Genet 2021; 59:605-612. [PMID: 33910934 DOI: 10.1136/jmedgenet-2020-107604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND A proportion of de novo variants in patients affected by genetic disorders, particularly those with autosomal dominant (AD) inheritance, could be the consequence of somatic mosaicism in one of the progenitors. There is growing evidence that germline and somatic mosaicism are more common and play a greater role in genetic disorders than previously acknowledged. In Marfan syndrome (MFS), caused by pathogenic variants in the fibrillin-1 gene (FBN1) gene, approximately 25% of the disease-causing variants are reported as de novo. Only a few cases of parental mosaicism have been reported in MFS. METHODS Employing an amplicon-based deep sequencing (ADS) method, we carried out a systematic analysis of 60 parents of 30 FBN1 positive, consecutive patients with MFS with an apparently de novo pathogenic variant. RESULTS Out of the 60 parents studied (30 families), the majority (n=51, 85%) had a systemic score of 0, seven had a score of 1 and two a score of 2, all due to minor criteria common in the normal population. We detected two families with somatic mosaicism in one of the progenitors, with a rate of 6.6% (2/30) of apparently de novo cases. CONCLUSIONS The search for parental somatic mosaicism should be routinely implemented in de novo cases of MFS, to offer appropriate genetic and reproductive counselling as well as to reveal masked, isolated clinical signs of MFS in progenitors that may require specific follow-up.
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Affiliation(s)
- Paula Fernández-Álvarez
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Marta Codina-Sola
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Gisela Teixidó-Turá
- Department of Cardiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Anna Cueto-González
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Ida Paramonov
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - María Antolín
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Fermina López-Grondona
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Teresa Vendrell
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Artur Evangelista
- Department of Cardiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Elena García-Arumí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Departament de Patologia Neuromuscular i Mitocondrial, Biomedical Network Research Centre on Rare Diseases (CIBERER), Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain .,Medicine Genetics Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
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27
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Chen W, Luo B, Gao N, Li H, Wang H, Li L, Cui W, Zhang L, Sun D, Liu F, Dong Z, Ren X, Zhang H, Su H, Xiong WC, Mei L. Neddylation stabilizes Nav1.1 to maintain interneuron excitability and prevent seizures in murine epilepsy models. J Clin Invest 2021; 131:136956. [PMID: 33651714 DOI: 10.1172/jci136956] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/23/2021] [Indexed: 12/19/2022] Open
Abstract
The excitability of interneurons requires Nav1.1, the α subunit of the voltage-gated sodium channel. Nav1.1 deficiency and mutations reduce interneuron excitability, a major pathological mechanism for epilepsy syndromes. However, the regulatory mechanisms of Nav1.1 expression remain unclear. Here, we provide evidence that neddylation is critical to Nav1.1 stability. Mutant mice lacking Nae1, an obligatory component of the E1 ligase for neddylation, in parvalbumin-positive interneurons (PVINs) exhibited spontaneous epileptic seizures and premature death. Electrophysiological studies indicate that Nae1 deletion reduced PVIN excitability and GABA release and consequently increased the network excitability of pyramidal neurons (PyNs). Further analysis revealed a reduction in sodium-current density, not a change in channel property, in mutant PVINs and decreased Nav1.1 protein levels. These results suggest that insufficient neddylation in PVINs reduces Nav1.1 stability and thus the excitability of PVINs; the ensuing increased PyN activity causes seizures in mice. Consistently, Nav1.1 was found reduced by proteomic analysis that revealed abnormality in synapses and metabolic pathways. Our findings describe a role of neddylation in maintaining Nav1.1 stability for PVIN excitability and reveal what we believe is a new mechanism in the pathogenesis of epilepsy.
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Affiliation(s)
- Wenbing Chen
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Bin Luo
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Nannan Gao
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Haiwen Li
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Hongsheng Wang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Lei Li
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wanpeng Cui
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Lei Zhang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dong Sun
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Fang Liu
- Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Zhaoqi Dong
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xiao Ren
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Hongsheng Zhang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Huabo Su
- Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Wen-Cheng Xiong
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Lin Mei
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
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28
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Shu L, Zhang Q, Tian Q, Yang S, Peng X, Mao X, Yang L, Du J, Wang H. Parental mosaicism in de novo neurodevelopmental diseases. Am J Med Genet A 2021; 185:2119-2125. [PMID: 33851778 DOI: 10.1002/ajmg.a.62174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/28/2021] [Accepted: 02/26/2021] [Indexed: 11/12/2022]
Abstract
Neurodevelopmental diseases are increasingly recognized to be caused by "de novo" variants with the expanding use of next-generation sequencing. The apparent de novo variants may actually be low-level hereditary parental mosaic variants, which could increase the recurrence risk of disease by >50% and is thought to be an underappreciated cause of neurodevelopmental diseases. Our study aimed to investigate the frequency of parental mosaicism in "de novo" neurodevelopmental diseases. A total of 237 patients (and parents) with neurodevelopmental diseases carrying apparent de novo pathogenic or likely pathogenic variants were recruited consecutively. Deep next-generation sequencing was performed on parental samples to identify parental mosaicism. Fourteen parental disease-causing mosaicism variants (3.0%) in 11 genes were detected with alternate allele frequency (AAF) 0.22%-34%. Three parents showed milder clinical phenotypes than their offspring with relatively high AAF (23.33%, 25%, 34% separately). One recurrent variant was identified prenatally. A review of cohort study on parental mosaicism in neurodevelopmental diseases was performed. Our study highlights that identifying the parental mosaic disease-causing variants especially the low-level mosaicism will contribute to improving the accuracy of genetic counseling and prenatal diagnosis for reproductive risks.
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Affiliation(s)
- Li Shu
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.,Department of School of Life Sciences, Central South University, Changsha, China
| | - Qianjun Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Medical Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
| | - Qi Tian
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Sai Yang
- Department of Neurology, Children's Hospital of Hunan Province, Changsha, China
| | - Xingwang Peng
- Marketing Management Center, AmCare Genomics Laboratory, Guangzhou, China
| | - Xiao Mao
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Liming Yang
- Department of Neurology, Children's Hospital of Hunan Province, Changsha, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Medical Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
| | - Hua Wang
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
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29
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Sullo F, Pasquetti E, Patanè F, Lo Bianco M, Marino SD, Polizzi A, Falsaperla R, Ruggieri M, Zanghì A, Praticò AD. SCN1A and Its Related Epileptic Phenotypes. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1727260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractEpilepsy is one of the most common neurological disorders, with a lifetime incidence of 1 in 26. Approximately two-thirds of epilepsy has a substantial genetic component in its etiology. As a result, simultaneous screening for mutations in multiple genes and performing whole exome sequencing (WES) are becoming very frequent in the clinical evaluation of children with epilepsy. In this setting, mutations in voltage-gated sodium channel (SCN) α-subunit genes are the most commonly identified cause of epilepsy, with sodium channel genes (i.e., SCN1A, SCN2A, SCN8A) being the most frequently identified causative genes. SCN1A mutations result in a wide spectrum of epilepsy phenotypes ranging from simple febrile seizures to Dravet syndrome, a severe epileptic encephalopathy. In case of mutation of SCN1A, it is also possible to observe behavioral alterations, such as impulsivity, inattentiveness, and distractibility, which can be framed in an attention deficit hyperactivity disorder (ADHD) like phenotype. Despite more than 1,200 SCN1A mutations being reported, it is not possible to assess a clear phenotype–genotype correlations. Treatment remains a challenge and seizure control is often partial and transitory.
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Affiliation(s)
- Federica Sullo
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Elisa Pasquetti
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Francesca Patanè
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Manuela Lo Bianco
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Simona D. Marino
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Agata Polizzi
- Chair of Pediatrics, Department of Educational Sciences, University of Catania, Catania, Italy
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
- Unit of Neonatal Intensive Care and Neonatology, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Martino Ruggieri
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Antonio Zanghì
- Department of Medical and Surgical Sciences and Advanced Technology “G.F. Ingrassia,” University of Catania, Catania, Italy
| | - Andrea D. Praticò
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
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30
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Ma H, Guo Y, Chen Z, Wang L, Tang Z, Zhang J, Miao Q, Zhai Q. Mutations in the sodium channel genes SCN1A, SCN3A, and SCN9A in children with epilepsy with febrile seizures plus(EFS+). Seizure 2021; 88:146-152. [PMID: 33895391 DOI: 10.1016/j.seizure.2021.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
PURPOSE To explore disease-causing gene mutations of epilepsy with febrile seizures plus (EFS+) in Southern Chinese Han population. METHODS Blood samples and clinical data were collected from 49 Southern Han Chinese patients with EFS+. Gene screening was performed using whole-exome sequencing and panel sequencing for 485 epilepsy-related genes. The pathogenicity of variants was evaluated based on ACMG scoring and assessment of clinical concordance. RESULTS We identified 10 putatively causative sodium channel gene variants in 49 patients with EFS+, including 8 variants in SCN1A (R500Q appeared twice), one in SCN3A and one in SCN9A. All these missense mutations were inherited from maternal or paternal and were evaluated to be of uncertain significance according to ACMG. The clinical features of patients were in concordance with the EFS+ phenotype of the mutated SCN1A, SCN3A and SCN9A gene. The clinical phenotypes of 11 probands with these gene variants included febrile seizures plus (FS+, n=7), Dravet Syndrome (n=3), FS+ with focal seizures (n=1). Three probands with SCN1A variants (R500Q located in the non-voltage areas, or G1711D in the pore-forming domain) developed severe Dravet syndrome. The affected individuals with the other 6 SCN1A variants located outside the pore-forming domain showed mild phenotypes. Novel SCN3A variant ((D1688Y) and SCN9A variant (R185H) were identified in two probands respectively and both of the probands had FS+. CONCLUSION The SCN1A, SCN3A, and SCN9A gene mutations might be a pathogenic cause of EFS+ in Southern Chinese Han population.
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Affiliation(s)
- Hongxia Ma
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, China; Department of Pediatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China; Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - Yuxiong Guo
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, China; Department of Pediatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Zhihong Chen
- Department of Pediatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Lingan Wang
- Department of Neurology and Rehabilitation, Guangdong Women and Children's Hospital, Guangzhou, Guangdong Province, China
| | - Zhihong Tang
- Department of Pediatrics, Dongguan City Maternal & Child Health Hospital, Dongguan, Guangdong Province, China
| | - Jingwen Zhang
- Department of Pediatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Qinfei Miao
- Shantou University, Shantou, Guangdong Province, China
| | - Qiongxiang Zhai
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, China; Department of Pediatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China.
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31
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Ding D, Zhou D, Sander JW, Wang W, Li S, Hong Z. Epilepsy in China: major progress in the past two decades. Lancet Neurol 2021; 20:316-326. [PMID: 33743240 DOI: 10.1016/s1474-4422(21)00023-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 12/15/2020] [Accepted: 01/07/2021] [Indexed: 02/08/2023]
Abstract
China has approximately 10 million people with epilepsy. There is a vast epilepsy treatment gap in China, mainly driven by deficiencies in health-care delivery and social discrimination resulting from cultural beliefs about epilepsy. WHO's Global Campaign Against Epilepsy project in China showed that it was possible to treat epilepsy in primary care settings, which was a notable milestone. The China Association Against Epilepsy has been a necessary force to stimulate interest in epilepsy care and research by the medical and scientific community. Nearly 20 different anti-seizure medications are now available in China. Non-pharmacological options are also available, but there are still unmet needs for epilepsy management. The Chinese epilepsy research portfolio is varied, but the areas in which there are the most concentrated focus and expertise are epidemiology and clinical research. The challenges for further improvement in delivering care for people with epilepsy in China are primarily related to public health and reducing inequalities within this vast country.
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Affiliation(s)
- Ding Ding
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Dong Zhou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
| | - Josemir W Sander
- NIHR University College London Hospitals Biomedical Research Centre, UCL Queen Square Institute of Neurology, London, UK; Chalfont Centre for Epilepsy, Chalfont St Peter, Buckinghamshire, UK; Stichting Epilepsie Instellingen Nederland, Heemstede, Netherlands.
| | - Wenzhi Wang
- Department of Neuroepidemiology, Beijing Neurosurgical Institute, Beijing, China
| | - Shichuo Li
- China Association against Epilepsy, Beijing, China
| | - Zhen Hong
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China
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32
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Antonarakis SE, Holoubek A, Rapti M, Rademaker J, Meylan J, Iwaszkiewicz J, Zoete V, Wilson C, Taylor J, Ansar M, Borel C, Menzel O, Kuželová K, Santoni FA. Dominant monoallelic variant in the PAK2 gene causes Knobloch syndrome type 2. Hum Mol Genet 2021; 31:1-9. [PMID: 33693784 DOI: 10.1093/hmg/ddab026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/11/2021] [Accepted: 01/31/2021] [Indexed: 11/12/2022] Open
Abstract
Knobloch syndrome is an autosomal recessive phenotype mainly characterized by retinal detachment and encephalocele caused by biallelic pathogenic variants in the COL18A1 gene. However, there are patients clinically diagnosed as Knobloch syndrome with unknown molecular etiology not linked to COL18A1. We studied an historical pedigree (published in 1998) designated as KNO2 (Knobloch type 2 syndrome with intellectual disability, autistic behavior, retinal degeneration, encephalocele). Whole exome sequencing of the two affected siblings and the normal parents resulted in the identification of a PAK2 non-synonymous substitution p.(Glu435Lys) as a causative variant. The variant was monoallelic and apparently de novo in both siblings indicating a likely germline mosaicism in one of the parents; the mosaicism however could not be observed after deep sequencing of blood parental DNA. PAK2 encodes a member of a small group of serine/threonine kinases; these P21-activating kinases (PAKs) are essential in signal transduction and cellular regulation (cytoskeletal dynamics, cell motility, death and survival signaling, and cell cycle progression). Structural analysis of the PAK2 p.(Glu435Lys) variant which is located in the kinase domain of the protein predicts a possible compromise in the kinase activity. Functional analysis of the p.(Glu435Lys) PAK2 variant in transfected HEK293T cells results in a partial loss of the kinase activity. PAK2 has been previously suggested as an autism related gene. Our results show that PAK2 induced phenotypic spectrum is broad and not fully understood. We conclude that the KNO2 syndrome in the studied family is dominant and caused by a deleterious variant in the PAK2 gene.
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Affiliation(s)
- Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva 1211, Switzerland
| | - Ales Holoubek
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Melivoia Rapti
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jesse Rademaker
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jenny Meylan
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Department of Fundamental Oncology, Ludwig Institute for Cancer Research, Lausanne University, Epalinges 1066, Switzerland
| | - Callum Wilson
- National Metabolic Service, Starship Children's Hospital, Auckland 1142, New Zealand
| | - Juliet Taylor
- National Metabolic Service, Starship Children's Hospital, Auckland 1142, New Zealand
| | - Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology, Basel 4031, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland
| | - Olivier Menzel
- Health 2030 Genome Center, Foundation Campus Biotech Geneva Foundation, Geneva 1202, Switzerland
| | - Kateřina Kuželová
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Federico A Santoni
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland.,Faculty of Biology and Medicine, University of Lausanne, Lausanne 1011, Switzerland
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33
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Moreno-García M, Arteche-López AR, Álvarez-Mora MI, Palma Milla C, Quesada Espinosa JF, Lezana Rosales JM, Sánchez Calvín MT, Gómez Manjón I, Gómez Rodríguez MJ, Mendez-Guerrero A, Villarejo-Galende A. First patient with mosaic NOTCH3 gene pathogenic variant. Unrevealed mosaicisms and importance of their detection. Am J Med Genet A 2020; 185:591-595. [PMID: 33305890 DOI: 10.1002/ajmg.a.61999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/06/2020] [Accepted: 11/14/2020] [Indexed: 01/14/2023]
Abstract
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited small vessel disease caused predominantly by pathogenic variants in NOTCH3 gene. Neither germline nor somatic mosaicism has been previously published in NOTCH3 gene. CADASIL is inherited in an autosomal dominant manner; only rare cases have been associated with de novo pathogenic variants. Mosaicism is more common than previously thought because mosaic variants often stay unrevealed. An apparently de novo variant might actually be a consequence of a parental mosaicism undetectable with Sanger sequencing, especially in the case of low grade mosaicism. Parental testing by sensitive tools like deep targeted next-generation sequencing (NGS) analysis could detect cases of unrevealed medium or low level mosaicism in patients tested by Sanger sequencing. Here, we report the first patient with mosaic NOTCH3 gene pathogenic variant to our knowledge; the allelic fraction in the leucocyte DNA was low (13%); the pathogenic variant was inhered by his two daughters. The patient was diagnosed by deep targeted NGS analysis after studying his two affected daughters. This report highlights the importance of parental testing by sensitive tools like deep targeted NGS analysis. Detection of mosaicism is of great importance for diagnosis and adequate family genetic counseling.
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Affiliation(s)
| | | | | | - Carmen Palma Milla
- Department of Genetics, University 12 de Octubre Hospital, Madrid, Spain
| | | | | | | | - Irene Gómez Manjón
- Department of Genetics, University 12 de Octubre Hospital, Madrid, Spain
| | | | | | - Alberto Villarejo-Galende
- Department of Neurology, University 12 de Octubre Hospital, Neurodegenerative Diseases Study Group, I+12, CIBERNED, Universidad Complutense, Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
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34
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Lin L, Zhang Y, Pan H, Wang J, Qi Y, Ma Y. Clinical and genetic characteristics and prenatal diagnosis of patients presented GDD/ID with rare monogenic causes. Orphanet J Rare Dis 2020; 15:317. [PMID: 33176815 PMCID: PMC7656751 DOI: 10.1186/s13023-020-01599-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
Background Global developmental delay/intellectual disability (GDD/ID), used to be named as mental retardation (MR), is one of the most common phenotypes in neurogenetic diseases. In this study, we described the diagnostic courses, clinical and genetic characteristics and prenatal diagnosis of a cohort with patients presented GDD/ID with monogenic causes, from the perspective of a tertiary genetic counseling and prenatal diagnostic center. Method We retrospectively analyzed the diagnostic courses, clinical characteristics, and genetic spectrum of patients presented GDD/ID with rare monogenic causes. We also conducted a follow-up study on prenatal diagnosis in these families. Pathogenicity of variants was interpreted by molecular geneticists and clinicians according to the guidelines of the American College of Medical Genetics and Genomics (ACMG). Results Among 81 patients with GDD/ID caused by rare monogenic variants it often took 0.5–4.5 years and 2–8 referrals to obtain genetic diagnoses. Devlopmental delay typically occurred before 3 years of age, and patients usually presented severe to profound GDD/ID. The most common co-existing conditions were epilepsy (58%), microcephaly (21%) and facial anomalies (17%). In total, 111 pathogenic variants were found in 62 different genes among the 81 pedigrees, and 56 variants were novel. The most common inheritance patterns in this outbred Chinese population were autosomal dominant (AD; 47%), following autosomal recessive (AR; 37%), and X-linked (XL; 16%). SCN2A, SHANK3 and STXBP1 were important causal genes. Hot-spot variants were rarely found. By the follow-up, 33 affected families, including 15, 13 and 5 families inherited in AR, AD and XL modes respectively, had undergone prenatal diagnosis. And the recurrence rates are 26.7%, 15.4% and 20% for families inherited in AR, AD, and XL patterns. Conclusion Patients presented with GDD/ID caused by rare single gene variants are characterized by early onset, relatively severe symptoms and great clinical variability and genetic heterogeneity. Timely referrals to genetic counseling and prenatal diagnostic laboratories are important for affected families planning to have additional children.
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Affiliation(s)
- Liling Lin
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Ying Zhang
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Hong Pan
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Yu Qi
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.
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35
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Vezyroglou A, Varadkar S, Bast T, Hirsch E, Strobl K, Harvey AS, Scheffer IE, Sisodiya SM, Cross JH. Focal epilepsy in SCN1A-mutation carrying patients: is there a role for epilepsy surgery? Dev Med Child Neurol 2020; 62:1331-1335. [PMID: 32538476 DOI: 10.1111/dmcn.14588] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/27/2020] [Indexed: 11/28/2022]
Abstract
Variants in the gene SCN1A are a common genetic cause for a wide range of epilepsy phenotypes ranging from febrile seizures to Dravet syndrome. Focal onset seizures and structural lesions can be present in these patients and the question arises whether epilepsy surgery should be considered. We report eight patients (mean age 13y 11mo [SD 8y 1mo], range 3-26y; four females, four males) with SCN1A variants, who underwent epilepsy surgery. Outcomes were variable and seemed to be directly related to the patient's anatomo-electroclinical epilepsy phenotype. Patients with Dravet syndrome had unfavourable outcomes, whilst patients with focal epilepsy, proven to arise from a single structural lesion, had good results. We conclude that the value of epilepsy surgery in patients with an SCN1A variant rests on two issues: understanding whether the variant is pathogenic and the patient's anatomo-electroclinical phenotype. Careful evaluation of epilepsy phenotype integrated with understanding the significance of genetic variants is essential in determining a patient's suitability for epilepsy surgery. Patients with focal onset epilepsy may benefit from epilepsy surgery, whereas those with Dravet syndrome do not. WHAT THIS PAPER ADDS: Patients should not automatically be excluded from epilepsy surgery evaluation if they carry an SCN1A variant. Patients with focal epilepsy may benefit from epilepsy surgery; those with Dravet syndrome do not.
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Affiliation(s)
- Aikaterini Vezyroglou
- Department of Developmental Neurosciences, UCL NIHR BRC Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Sophia Varadkar
- Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Thomas Bast
- Kork Epilepsy Center, Kehl-Kork, Germany.,Medical Faculty of the University of Freiburg, Freiburg, Germany
| | - Edouard Hirsch
- Medical and Surgical Epilepsy Unit, Hautepierre Hospital, University of Strasbourg, Strasbourg, France
| | | | - A Simon Harvey
- Department of Neurology, The Royal Children's Hospital, Melbourne, Victoria, Australia
| | | | - Ingrid E Scheffer
- Department of Neurology, The Royal Children's Hospital, Melbourne, Victoria, Australia.,Florey Institute and Murdoch Children's Research Institute, Austin Health and Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - J Helen Cross
- Department of Developmental Neurosciences, UCL NIHR BRC Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital for Children, London, UK
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36
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MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:140-149. [PMID: 32911083 PMCID: PMC7646124 DOI: 10.1016/j.gpb.2020.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 03/18/2020] [Accepted: 05/31/2020] [Indexed: 12/14/2022]
Abstract
Mosaic variants resulting from postzygotic mutations are prevalent in the human genome and play important roles in human diseases. However, except for cancer-related variants, there is no collection of postzygotic mosaic variants in noncancer disease-related and healthy individuals. Here, we present MosaicBase, a comprehensive database that includes 6698 mosaic variants related to 266 noncancer diseases and 27,991 mosaic variants identified in 422 healthy individuals. Genomic and phenotypic information of each variant was manually extracted and curated from 383 publications. MosaicBase supports the query of variants with Online Mendelian Inheritance in Man (OMIM) entries, genomic coordinates, gene symbols, or Entrez IDs. We also provide an integrated genome browser for users to easily access mosaic variants and their related annotations for any genomic region. By analyzing the variants collected in MosaicBase, we find that mosaic variants that directly contribute to disease phenotype show features distinct from those of variants in individuals with mild or no phenotypes, in terms of their genomic distribution, mutation signatures, and fraction of mutant cells. MosaicBase will not only assist clinicians in genetic counseling and diagnosis but also provide a useful resource to understand the genomic baseline of postzygotic mutations in the general human population. MosaicBase is publicly available at http://mosaicbase.com/ or http://49.4.21.8:8000.
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37
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Menezes LFS, Sabiá Júnior EF, Tibery DV, Carneiro LDA, Schwartz EF. Epilepsy-Related Voltage-Gated Sodium Channelopathies: A Review. Front Pharmacol 2020; 11:1276. [PMID: 33013363 PMCID: PMC7461817 DOI: 10.3389/fphar.2020.01276] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/31/2020] [Indexed: 12/29/2022] Open
Abstract
Epilepsy is a disease characterized by abnormal brain activity and a predisposition to generate epileptic seizures, leading to neurobiological, cognitive, psychological, social, and economic impacts for the patient. There are several known causes for epilepsy; one of them is the malfunction of ion channels, resulting from mutations. Voltage-gated sodium channels (NaV) play an essential role in the generation and propagation of action potential, and malfunction caused by mutations can induce irregular neuronal activity. That said, several genetic variations in NaV channels have been described and associated with epilepsy. These mutations can affect channel kinetics, modifying channel activation, inactivation, recovery from inactivation, and/or the current window. Among the NaV subtypes related to epilepsy, NaV1.1 is doubtless the most relevant, with more than 1500 mutations described. Truncation and missense mutations are the most observed alterations. In addition, several studies have already related mutated NaV channels with the electrophysiological functioning of the channel, aiming to correlate with the epilepsy phenotype. The present review provides an overview of studies on epilepsy-associated mutated human NaV1.1, NaV1.2, NaV1.3, NaV1.6, and NaV1.7.
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Affiliation(s)
- Luis Felipe Santos Menezes
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | - Elias Ferreira Sabiá Júnior
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | - Diogo Vieira Tibery
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | - Lilian Dos Anjos Carneiro
- Faculdade de Medicina, Centro Universitário Euro Americano, Brasília, Brazil.,Faculdade de Medicina, Centro Universitário do Planalto Central, Brasília, Brazil
| | - Elisabeth Ferroni Schwartz
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
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38
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Heinzen EL. Somatic variants in epilepsy - advancing gene discovery and disease mechanisms. Curr Opin Genet Dev 2020; 65:1-7. [PMID: 32422520 DOI: 10.1016/j.gde.2020.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/15/2020] [Indexed: 01/03/2023]
Abstract
In the past ten years, there has been increasing recognition that cells can acquire genetic variants during cortical development that can give rise to brain malformations as well as nonlesional focal epilepsy. These often brain tissue-specific, de novo variants can result in highly variable phenotypes based on the burden of a variant in specific tissues and cells. By discovering these variants, shared pathophysiological mechanisms are being revealed between clinically distinct disorders. Beyond informing disease mechanisms, mosaic variants also offer a powerful research tool to trace cellular lineages, to study the roles of specialized cell types in disease presentation, and to establish the cell-type specific genomic consequences of a variant.
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Affiliation(s)
- Erin L Heinzen
- Eshelman School of Pharmacy, Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, NC, United States; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, United States.
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39
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Mei D, Cetica V, Marini C, Guerrini R. Dravet syndrome as part of the clinical and genetic spectrum of sodium channel epilepsies and encephalopathies. Epilepsia 2020; 60 Suppl 3:S2-S7. [PMID: 31904125 DOI: 10.1111/epi.16054] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 01/01/2023]
Abstract
Dravet syndrome is the most studied form of genetic epilepsy. It has now been clarified that the clinical spectrum of the syndrome does not have firmly established boundaries. The core phenotype is characterized by intractable, mainly clonic, seizures precipitated by increased body temperature with onset in the first year of life and subsequent appearance of multiple seizures types still precipitated by, but not confined to, hyperthermia. Cognitive impairment is invariably present when the full syndrome is manifested. This complex of symptoms is related to mutations in the SCN1A gene, which are often de novo and constitutional but can also be inherited from a parent with less severe clinical manifestations or be present as somatic mosaicism. Inheritance from less severely affected individuals, at times only having experienced a few febrile seizures, and differences in severity, even within the same family, with a subset of patients only showing fragments of the syndrome, testify to a remarkable phenotypic heterogeneity as far as severity, but less so clinical phenomenology, are concerned. This characteristic, together with underascertainment of SCN1A mutations due to human errors or technical limitations in uncovering alternative pathogenic molecular mechanisms, such as genomic rearrangements or poison exons, has contributed to making clinicians and geneticists suspicious that Dravet syndrome may be caused by more than one gene. This opinion has been further amplified by the description of other genetic disorders, such as PCDH19- or CHD2-related epilepsy, whose phenotypes have included fragments of the Dravet phenotypic spectrum, and by the suboptimal characterization of phenotypes associated with mutations in SCN1B, HCN1, KCN2A, GABRA1, GABRG2, and STXBP1. The SCN1A gene-Dravet syndrome association is in our opinion highly specific. However, because the syndrome spectrum is wide, fragments of it can at times also be manifested in other genetic epilepsy syndromes, thereby leading to overdiagnosis of Dravet syndrome beyond SCN1A. Dravet syndrome is in turn a severe SCN1A phenotype within a continuum of SCN1A-related clinical phenomenology.
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Affiliation(s)
- Davide Mei
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories, Meyer Children's Hospital-University of Florence, Florence, Italy
| | - Valentina Cetica
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories, Meyer Children's Hospital-University of Florence, Florence, Italy
| | - Carla Marini
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories, Meyer Children's Hospital-University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories, Meyer Children's Hospital-University of Florence, Florence, Italy.,IRCCS Stella Maris Foundation, Pisa, Italy
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40
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Brewer CJ, Gillespie M, Fierro J, Scaringe WA, Li JM, Lee CY, Yen HY, Gao H, Strom SP. The Value of Parental Testing by Next-Generation Sequencing Includes the Detection of Germline Mosaicism. J Mol Diagn 2020; 22:670-678. [PMID: 32092540 DOI: 10.1016/j.jmoldx.2020.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/27/2020] [Accepted: 02/04/2020] [Indexed: 10/25/2022] Open
Abstract
When a potential disease-causing variant is detected in a proband, parental testing is used to determine the mode of inheritance. This study demonstrates that next-generation sequencing (NGS) is uniquely well suited for parental testing, in particular because of its ability to detect clinically relevant germline mosaicism. Parental variant testing by NGS was performed in a clinical laboratory for 1 year. The detection of mosaicism by NGS was compared with its detection by Sanger sequencing. Eight cases of previously unrevealed mosaicism were detected by NGS across eight different genes. Mosaic variants were differentiated from sequencing noise using custom bioinformatics analyses in combination with familial inheritance data and complementary Sanger sequencing. Sanger sequencing detected mosaic variants with allele fractions ≥8% by NGS, but could not detect mosaic variants below that level. Detection of germline mosaicism by NGS is invaluable to parents, providing a more accurate recurrence risk that can alter decisions on family planning and pregnancy management. Because NGS can also confirm parentage and increase scalability, it simultaneously streamlines and strengthens the variant curation process. These features make NGS the ideal method for parental testing, superior even to Sanger sequencing for most genomic loci.
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Affiliation(s)
| | | | | | | | | | - Che-Yu Lee
- Fulgent Genetics, Temple City, California
| | | | - Hanlin Gao
- Fulgent Genetics, Temple City, California
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41
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Rivière JG, Franco-Jarava C, Martínez-Gallo M, Aguiló-Cucurull A, Blasco-Pérez L, Paramonov I, Antolín M, Martín-Nalda A, Soler-Palacín P, Colobran R. Uncovering Low-Level Maternal Gonosomal Mosaicism in X-Linked Agammaglobulinemia: Implications for Genetic Counseling. Front Immunol 2020; 11:46. [PMID: 32117230 PMCID: PMC7028698 DOI: 10.3389/fimmu.2020.00046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/09/2020] [Indexed: 11/20/2022] Open
Abstract
X-linked agammaglobulinemia (XLA) is a clinically and genetically well-defined immunodeficiency and the most common form of agammaglobulinemia. It is characterized by susceptibility to recurrent bacterial infections, profound hypogammaglobulinemia, and few or no circulating B cells. XLA is caused by mutations in the BTK gene, which encodes Bruton's tyrosine kinase (BTK). Because of its X-linked recessive inheritance pattern, XLA virtually only affects males, and the mother is the carrier of the mutation in 80–85% of the males with this condition. In the remaining 15–20% of the cases, the affected male is considered to have a de novo mutation. Here, we present the case of a child with a diagnosis of XLA caused by a missense mutation in the BTK gene (c.494G>A/p.C165Y). Apparently, his mother was wild type for this gene, which implied that the mutation was de novo, but careful analysis of Sanger electropherograms and the use of high-coverage massive parallel sequencing revealed low-level maternal gonosomal mosaicism. The mutation was detected in various samples from the mother (blood, urine, buccal swab, and vaginal swab) at a low frequency of 2–5%, and the status of the patient's mutation changed from de novo to inherited. This study underscores the importance of accurately establishing the parents' status on detection of an apparently de novo mutation in a patient, as inadvertent low-level mosaicism may lead to misinterpretation of the risk of recurrence, vital for genetic counseling.
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Affiliation(s)
- Jacques G Rivière
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Clara Franco-Jarava
- Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Immunology Division, Department of Cell Biology, Physiology and Immunology, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Immunology Division, Department of Cell Biology, Physiology and Immunology, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain
| | - Aina Aguiló-Cucurull
- Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Immunology Division, Department of Cell Biology, Physiology and Immunology, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain
| | - Laura Blasco-Pérez
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ida Paramonov
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - María Antolín
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Roger Colobran
- Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Immunology Division, Department of Cell Biology, Physiology and Immunology, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain.,Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain
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Abstract
Epilepsy is considered a disease characterized by an underlying predisposition to seizures as well as neurobiologic, cognitive, psychologic, and social consequences. It is the most frequent chronic neurologic condition of childhood, affecting 0.5%-1% of children worldwide. It comprises a variety of disorders with many different etiologies, consequently affecting management and outcome. Although the great majority of children have epilepsies that are self-limited and have a good prognosis, it is nevertheless very well recognized that epileptic activity (be it seizures or interictal discharges) can be particularly deleterious to the developing brain acting as a disruptor to normal developmental function. Indeed, epilepsy and neurocognitive and behavioral disorders very frequently coexist, and it can be challenging to understand if there is causality or if they are all the reflection of the underlying brain disorder. Hence, accurate phenotypic and etiologic diagnosis is of utmost importance as it will not only guide decision making with regard to choice of treatment but also enable management of expectations concerning outcome. The current chapter aims to provide a general overview of the fast evolving and vast field of childhood epilepsy from its definition and epidemiology, to its diagnostic challenges, management, and outcome.
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Affiliation(s)
- Filipa Bastos
- University College London National Institute of Health Research Biomedical Research Centre, Great Ormond Street Institute of Child Health, and Great Ormond Street Hospital for Children NHS Trust, London, United Kingdom; Centre Hospitalier Universitaire de Lausanne, Child Neurology and Neurorehabilitation Unit, University of Lausanne, Lausanne, Switzerland
| | - J Helen Cross
- University College London National Institute of Health Research Biomedical Research Centre, Great Ormond Street Institute of Child Health, and Great Ormond Street Hospital for Children NHS Trust, London, United Kingdom.
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43
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Breuss MW, Antaki D, George RD, Kleiber M, James KN, Ball LL, Hong O, Mitra I, Yang X, Wirth SA, Gu J, Garcia CAB, Gujral M, Brandler WM, Musaev D, Nguyen A, McEvoy-Venneri J, Knox R, Sticca E, Botello MCC, Uribe Fenner J, Pérez MC, Arranz M, Moffitt AB, Wang Z, Hervás A, Devinsky O, Gymrek M, Sebat J, Gleeson JG. Autism risk in offspring can be assessed through quantification of male sperm mosaicism. Nat Med 2020; 26:143-150. [PMID: 31873310 PMCID: PMC7032648 DOI: 10.1038/s41591-019-0711-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/21/2019] [Indexed: 01/28/2023]
Abstract
De novo mutations arising on the paternal chromosome make the largest known contribution to autism risk, and correlate with paternal age at the time of conception. The recurrence risk for autism spectrum disorders is substantial, leading many families to decline future pregnancies, but the potential impact of assessing parental gonadal mosaicism has not been considered. We measured sperm mosaicism using deep-whole-genome sequencing, for variants both present in an offspring and evident only in father's sperm, and identified single-nucleotide, structural and short tandem-repeat variants. We found that mosaicism quantification can stratify autism spectrum disorders recurrence risk due to de novo mutations into a vast majority with near 0% recurrence and a small fraction with a substantially higher and quantifiable risk, and we identify novel mosaic variants at risk for transmission to a future offspring. This suggests, therefore, that genetic counseling would benefit from the addition of sperm mosaicism assessment.
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Affiliation(s)
- Martin W Breuss
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Danny Antaki
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Renee D George
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Morgan Kleiber
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kiely N James
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Laurel L Ball
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Oanh Hong
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ileena Mitra
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara A Wirth
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jing Gu
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Camila A B Garcia
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Madhusudan Gujral
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - William M Brandler
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Damir Musaev
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - An Nguyen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Renatta Knox
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Child Neurology, Weill Cornell Medical College, New York, NY, USA
| | - Evan Sticca
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Javiera Uribe Fenner
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | | | - Maria Arranz
- Fundació Docència i Recerca Mútua Terrassa, Barcelona, Spain
| | - Andrea B Moffitt
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Amaia Hervás
- Research Laboratory Unit, Fundació Docencia i Recerca Mútua Terrassa, Barcelona, Spain
| | - Orrin Devinsky
- Department of Neurology, Epilepsy Division, New York University School of Medicine, New York, NY, USA
| | - Melissa Gymrek
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA.
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Joseph G Gleeson
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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44
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Tan RYY, Traylor M, Megy K, Duarte D, Deevi SVV, Shamardina O, Mapeta RP, Ouwehand WH, Gräf S, Downes K, Markus HS. How common are single gene mutations as a cause for lacunar stroke? A targeted gene panel study. Neurology 2019; 93:e2007-e2020. [PMID: 31719132 PMCID: PMC6913325 DOI: 10.1212/wnl.0000000000008544] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022] Open
Abstract
Objectives To determine the frequency of rare and pertinent disease-causing variants in small vessel disease (SVD)-associated genes (such as NOTCH3, HTRA1, COL4A1, COL4A2, FOXC1, TREX1, and GLA) in cerebral SVD, we performed targeted gene sequencing in 950 patients with younger-onset apparently sporadic SVD stroke using a targeted sequencing panel. Methods We designed a high-throughput sequencing panel to identify variants in 15 genes (7 known SVD genes, 8 SVD-related disorder genes). The panel was used to screen a population of 950 patients with younger-onset (≤70 years) MRI-confirmed SVD stroke, recruited from stroke centers across the United Kingdom. Variants were filtered according to their frequency in control databases, predicted effect, presence in curated variant lists, and combined annotation dependent depletion scores. Whole genome sequencing and genotyping were performed on a subset of patients to provide a direct comparison of techniques. The frequency of known disease-causing and pertinent variants of uncertain significance was calculated. Results We identified previously reported variants in 14 patients (8 cysteine-changing NOTCH3 variants in 11 patients, 2 HTRA1 variants in 2 patients, and 1 missense COL4A1 variant in 1 patient). In addition, we identified 29 variants of uncertain significance in 32 patients. Conclusion Rare monogenic variants account for about 1.5% of younger onset lacunar stroke. Most are cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy variants, but the second most common gene affected is HTRA1. A high-throughput sequencing technology platform is an efficient, reliable method to screen for such mutations.
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Affiliation(s)
- Rhea Y Y Tan
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK.
| | - Matthew Traylor
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
| | - Karyn Megy
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
| | - Daniel Duarte
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
| | - Sri V V Deevi
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
| | - Olga Shamardina
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
| | - Rutendo P Mapeta
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
| | | | - Willem H Ouwehand
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
| | - Stefan Gräf
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
| | - Kate Downes
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
| | - Hugh S Markus
- From the Stroke Research Group, Department of Clinical Neurosciences (R.Y.Y.T., M.T., H.S.M.), Department of Haematology (K.M., D.D., S.V.V.D., O.S., R.P.M., W.H.O., S.G., K.D.), and Division of Respiratory Medicine, Department of Medicine (S.G.), University of Cambridge; and NIHR BioResource: Rare Diseases (K.M., S.V.V.D., O.S., R.P.M., W.H.O., S.G., H.S.M.), Biomedical Campus, Cambridge, UK
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Ponard D, Gaboriaud C, Charignon D, Ghannam A, Wagenaar-Bos IGA, Roem D, López-Lera A, López-Trascasa M, Tosi M, Drouet C. SERPING1 mutation update: Mutation spectrum and C1 Inhibitor phenotypes. Hum Mutat 2019; 41:38-57. [PMID: 31517426 DOI: 10.1002/humu.23917] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022]
Abstract
C1 inhibitor (C1Inh) deficiency is responsible for hereditary angioedema (C1-INH-HAE) and caused by variants of the SERPING1/C1INH/C1NH gene. C1Inh is the major control of kallikrein-kinin system. C1Inh deficiency leads to its uncontrolled activation, with subsequent generation of the vasoactive peptide bradykinin. This update documents 748 different SERPING1 variants, including published variants and additional 120 unpublished ones. They were identified as heterozygous variants (n = 729), as homozygous variants in 10 probands and as compound heterozygous variants (nine combinations). Six probands with heterozygous variants exhibited gonadal mosaicism. Probands with heterozygous (n = 72) and homozygous (n = 1) variants were identified as de novo cases. Overall, 58 variants were found at positions showing high residue conservation among serpins, and have been referred to as a mousetrap function of C1Inh: reactive center loop, gate, shutter, breach, and hinge. C1Inh phenotype analysis identified dysfunctional serpin variants with failed serpin-protease association and a residual 105-kDa species after incubation with target protease. Regarding this characteristic, in conditions with low antigenic C1Inh, 74 C1-INH-HAE probands presented with an additional so-called intermediate C1-INH-HAE phenotype. The present update addresses a comprehensive SERPING1 variant spectrum that facilitates genotype-phenotype correlations, highlighting residues of strategic importance for serpin function and for identification of C1Inh deficiency as serpinopathy.
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Affiliation(s)
- Denise Ponard
- Centre de Référence des Angioedèmes (CREAK), Filière MaRIH, CHU Grenoble, Grenoble, France.,Laboratoire d'Immunologie, CHU Grenoble Alpes, Grenoble, France
| | | | - Delphine Charignon
- GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,KininX SAS, Grenoble, France
| | - Arije Ghannam
- GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,KininX SAS, Grenoble, France
| | | | - Dorina Roem
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands
| | - Alberto López-Lera
- Biomedical Research Network on Rare Diseases (CIBERER)-U754, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | | | - Mario Tosi
- Inserm U1245, University of Rouen, Rouen, France
| | - Christian Drouet
- Centre de Référence des Angioedèmes (CREAK), Filière MaRIH, CHU Grenoble, Grenoble, France.,GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,Inserm U1016, CNRS UMR8104, Institut Cochin, Université Paris-Descartes, France
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46
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Jang SS, Kim SY, Kim H, Hwang H, Chae JH, Kim KJ, Kim JI, Lim BC. Diagnostic Yield of Epilepsy Panel Testing in Patients With Seizure Onset Within the First Year of Life. Front Neurol 2019; 10:988. [PMID: 31572294 PMCID: PMC6753218 DOI: 10.3389/fneur.2019.00988] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/29/2019] [Indexed: 11/13/2022] Open
Abstract
Purpose: We aimed to evaluate the diagnostic yield of epilepsy gene panel testing in epilepsy patients whose seizures began within the first year after birth. We included 112 patients with seizure onset before 12 months and no known etiology. Methods: Deep targeted sequencing with a custom-designed capture probe was performed to ensure the detection of germline or mosaic sequence variants and copy number variations (CNVs). Results: We identified pathogenic or likely pathogenic variants in 53 patients (47.3%, 53/112), including five with pathogenic CNVs. Two putative pathogenic mosaic variants in SCN8A and KCNQ2 were also detected and validated. Those with neonatal onset (61.5%, 16/26) or early infantile onset (50.0%, 29/58) showed higher diagnostic rates than those with late infantile onset (28.5%, 8/28). The diagnostic rate was similar between patients with a specific syndrome (51.9%, 27/52) and those with no recognizable syndrome (43.3%, 26/60). Conclusion: Epilepsy gene panel testing identified a genetic cause in nearly half of the infantile onset epilepsy patients. Since the phenotypic spectrum is expanding and characterizing it at seizure onset is difficult, this group should be prioritized for epilepsy gene panel testing.
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Affiliation(s)
- Se Song Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Soo Yeon Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Hunmin Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Bundang-gu, South Korea
| | - Hee Hwang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Bundang-gu, South Korea
| | - Jong Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Ki Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea.,Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, South Korea.,Medical Research Center, Genomic Medicine Institute, Seoul National University, Seoul, South Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
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47
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Sanchis-Juan A, Bitsara C, Low KY, Carss KJ, French CE, Spasic-Boskovic O, Jarvis J, Field M, Raymond FL, Grozeva D. Rare Genetic Variation in 135 Families With Family History Suggestive of X-Linked Intellectual Disability. Front Genet 2019; 10:578. [PMID: 31316545 PMCID: PMC6609311 DOI: 10.3389/fgene.2019.00578] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/03/2019] [Indexed: 01/08/2023] Open
Abstract
Families with multiple male children with intellectual disability (ID) are usually suspected of having disease due to a X-linked mode of inheritance and genetic studies focus on analysis of segregating variants in X-linked genes. However, the genetic cause of ID remains elusive in approximately 50% of affected individuals. Here, we report the analysis of next-generation sequencing data in 274 affected individuals from 135 families with a family history suggestive of X-linked ID. Genetic diagnoses were obtained for 19% (25/135) of the families, and 24% (33/135) had a variant of uncertain significance. In 12% of cases (16/135), the variants were not shared within the family, suggesting genetic heterogeneity and phenocopies are frequent. Of all the families with reportable variants (43%, 58/135), we observed that 55% (32/58) were in X-linked genes, but 38% (22/58) were in autosomal genes, while the remaining 7% (4/58) had multiple variants in genes with different modes on inheritance. This study highlights that in families with multiple affected males, X linkage should not be assumed, and both individuals should be considered, as different genetic etiologies are common in apparent familial cases.
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Affiliation(s)
- Alba Sanchis-Juan
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, United Kingdom.,Cambridge University Hospitals NHS Foundation Trust, NIHR BioResource, Cambridge, United Kingdom
| | - Christina Bitsara
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Kay Yi Low
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Keren J Carss
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, United Kingdom.,Cambridge University Hospitals NHS Foundation Trust, NIHR BioResource, Cambridge, United Kingdom
| | - Courtney E French
- Cambridge University Hospitals NHS Foundation Trust, NIHR BioResource, Cambridge, United Kingdom.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Olivera Spasic-Boskovic
- East Anglian Medical Genetics Service, Cambridge University Hospital, Cambridge, United Kingdom
| | - Joanna Jarvis
- Clinical Genetics Unit, Birmingham Women's NHS Foundation Trust, Birmingham, United Kingdom
| | - Michael Field
- Genetics of Learning Disability Service (Hunter Genetics), Waratah, NSW, Australia
| | - F Lucy Raymond
- Cambridge University Hospitals NHS Foundation Trust, NIHR BioResource, Cambridge, United Kingdom.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Detelina Grozeva
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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48
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Møller RS, Liebmann N, Larsen LHG, Stiller M, Hentschel J, Kako N, Abdin D, Di Donato N, Pal DK, Zacher P, Syrbe S, Dahl HA, Lemke JR. Parental mosaicism in epilepsies due to alleged de novo variants. Epilepsia 2019; 60:e63-e66. [PMID: 31077350 DOI: 10.1111/epi.15187] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/02/2019] [Accepted: 04/15/2019] [Indexed: 02/03/2023]
Abstract
Severe early onset epilepsies are often caused by de novo pathogenic variants. Few studies have reported the frequency of somatic mosaicism in parents of children with severe epileptic encephalopathies. Here we aim to investigate the frequency of mosaicism in the parents of children with epilepsy caused by alleged de novo variants. We tested parental genomic DNA derived from different tissues for 75 cases using targeted next-generation sequencing. Five parents (6.6%) showed mosaicism at minor allele frequencies of 0.8%-29% for the pathogenic variant detected in their offspring. Parental mosaicism was observed in the following genes: SCN1A, SCN2A, SCN8A, and STXBP1. One of the identified parents had epilepsy himself. Our results show that de novo events can occur already in parental tissue and in some cases can be detected in peripheral blood. Consequently, parents affected by low-grade mosaicism are faced with an increased recurrence risk for transmitting the pathogenic variant, compared to the overall recurrence risk for a second affected child estimated at approximately 1%. However, testing for parental somatic mosaicism will help identifying those parents who truly are at higher risk and will significantly improve genetic counseling in the respective families.
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Affiliation(s)
- Rikke S Møller
- Danish Epilepsy Centre, Dianalund, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Nora Liebmann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Mathias Stiller
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Dalia Abdin
- Institute for Clinical Genetics, TU Dresden, Dresden, Germany
| | | | - Deb K Pal
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- King's College Hospital, London, UK
- Evelina London Children's Hospital, London, UK
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Steffen Syrbe
- Department of General Paediatrics, Division of Child Neurology and Inherited Metabolic Diseases, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
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49
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Yang X, Yang X, Chen J, Li S, Zeng Q, Huang AY, Ye AY, Yu Z, Wang S, Jiang Y, Wu X, Wu Q, Wei L, Zhang Y. ATP1A3 mosaicism in families with alternating hemiplegia of childhood. Clin Genet 2019; 96:43-52. [PMID: 30891744 PMCID: PMC6850116 DOI: 10.1111/cge.13539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 03/10/2019] [Accepted: 03/15/2019] [Indexed: 01/17/2023]
Abstract
Alternating hemiplegia of childhood (AHC) is a rare and severe neurodevelopmental disorder characterized by recurrent hemiplegic episodes. Most AHC cases are sporadic and caused by de novo ATP1A3 pathogenic variants. In this study, the aim was to identify the origin of ATP1A3 pathogenic variants in a Chinese cohort. In 105 probands including 101 sporadic and 4 familial cases, 98 patients with ATP1A3 pathogenic variants were identified, and 96.8% were confirmed as de novo. Micro-droplet digital polymerase chain reaction was applied for detecting ATP1A3 mosaicism in 80 available families. In blood samples, four asymptomatic parents, including two paternal and two maternal, and one proband with a milder phenotype were identified as mosaicism. Six (7.5%) parental mosaicisms were identified in multiple tissues, including four previously identified in blood and two additional cases identified from paternal sperms. Mosaicism was identified in multiple tissues with varied mutant allele fractions (MAFs, 0.03%-33.03%). The results suggested that MAF of mosaicism may be related to phenotype severity. This is the first systematic report of ATP1A3 mosaicism in AHC and showed mosaicism as an unrecognized source of previously considered "de novo" AHC. Identifying ATP1A3 mosaicism provides more evidence for estimating recurrence risk and has implications in genetic counseling of AHC.
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Affiliation(s)
- Xiaoling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jiaoyang Chen
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Shupin Li
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Qi Zeng
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - August Y Huang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Adam Y Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhe Yu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Sheng Wang
- Dr Liping Wei's lab, National Institute of Biological Sciences, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiru Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Qixi Wu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Human Genetic Resources Core Facility, School of Life Sciences, Peking University, Beijing, China
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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50
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Belousova ED, Sharkov AA. [Difficulties in the diagnosis, prognosis and treatment of genetic epileptic encephalopathies: the view of a neurologist]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:34-40. [PMID: 32207729 DOI: 10.17116/jnevro201911911234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic epileptic encephalopathies are a rather wide spectrum of childhood epilepsies with onset of epilepsy in the first 1.5-2 years of life, regression or delayed psychomotor and speech development and 'massive' epileptiform activity on electroencephalogram (EEG). The review discusses the difficulties of choosing the optimal method of genetic examination, problems with the interpretation of the results obtained, the formulation of the diagnosis, the determination of the prognosis of the course and targeted therapy. It is emphasized that the interpretation of the identified genetic variants is not an easy task, requiring close interaction between specialists in molecular genetics, bioinformatics, neurology and clinical genetics. The possibilities of targeted treatment of genetic epileptic encephalopathies are still limited, but knowledge of the genetic cause of epilepsy allows making a more informed choice of the treatment.
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Affiliation(s)
- E D Belousova
- Veltischev Research and Clinical Institute of Pediatrics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - A A Sharkov
- Veltischev Research and Clinical Institute of Pediatrics, Pirogov Russian National Research Medical University, Moscow, Russia
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