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Yang X, Mao Y, Wang XK, Ma DN, Xu Z, Gong N, Henning B, Zhang X, He G, Shi YY, Eichler EE, Li ZQ, Takahashi E, Li WD. Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing. Zool Res 2023; 44:837-847. [PMID: 37501399 PMCID: PMC10559097 DOI: 10.24272/j.issn.2095-8137.2022.514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
The common marmoset ( Callithrix jacchus) has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies. Epileptic marmosets have been independently reported in two Asian primate research centers. Nevertheless, the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated. Here, we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing. We identified 14 558 184 single nucleotide polymorphisms (SNPs) from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples. Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers. In addition, SNP and copy number variation (CNV) analyses suggested that the WW domain-containing oxidoreductase ( WWOX) and Tyrosine-protein phosphatase nonreceptor type 21 ( PTPN21) genes may be associated with epilepsy in marmosets. Notably, KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets. This study provides valuable population genomic resources for marmosets in two Asian primate centers. Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers, while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.
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Affiliation(s)
- XiangYu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai 200030, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
| | - YaFei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Genome Sciences, University of Washington School of Medicine, Seattle WA 98195, USA
| | - Xuan-Kai Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dong-Ni Ma
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
| | - Zhen Xu
- Institute of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Neng Gong
- Institute of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Barbara Henning
- Department of Genome Sciences, University of Washington School of Medicine, Seattle WA 98195, USA
| | - Xu Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong-Yong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Affiliated Hospital of Qingdao University & Biomedical Sciences Institute of Qingdao University, Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, Shandong 266003, China
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle WA 98195, USA
| | - Zhi-Qiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Affiliated Hospital of Qingdao University & Biomedical Sciences Institute of Qingdao University, Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, Shandong 266003, China. E-mail:
| | - Eiki Takahashi
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Biomedicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan. E-mail:
| | - Wei-Dong Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai 200030, China
- WLA Laboratories, World Laureates Association, Shanghai 201203, China
- Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai 200240, China. E-mail:
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2
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Salpietro V, Galassi Deforie V, Efthymiou S, O'Connor E, Marcé‐Grau A, Maroofian R, Striano P, Zara F, Morrow MM, Reich A, Blevins A, Sala‐Coromina J, Accogli A, Fortuna S, Alesandrini M, Au PYB, Singhal NS, Cogne B, Isidor B, Hanna MG, Macaya A, Kullmann DM, Houlden H, Männikkö R. De novo KCNA6 variants with attenuated K V 1.6 channel deactivation in patients with epilepsy. Epilepsia 2023; 64:443-455. [PMID: 36318112 PMCID: PMC10108282 DOI: 10.1111/epi.17455] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Mutations in the genes encoding neuronal ion channels are a common cause of Mendelian neurological diseases. We sought to identify novel de novo sequence variants in cases with early infantile epileptic phenotypes and neurodevelopmental anomalies. METHODS Following clinical diagnosis, we performed whole exome sequencing of the index cases and their parents. Identified channel variants were expressed in Xenopus oocytes and their functional properties assessed using two-electrode voltage clamp. RESULTS We identified novel de novo variants in KCNA6 in four unrelated individuals variably affected with neurodevelopmental disorders and seizures with onset in the first year of life. Three of the four identified mutations affect the pore-lining S6 α-helix of KV 1.6. A prominent finding of functional characterization in Xenopus oocytes was that the channel variants showed only minor effects on channel activation but slowed channel closure and shifted the voltage dependence of deactivation in a hyperpolarizing direction. Channels with a mutation affecting the S6 helix display dominant effects on channel deactivation when co-expressed with wild-type KV 1.6 or KV 1.1 subunits. SIGNIFICANCE This is the first report of de novo nonsynonymous variants in KCNA6 associated with neurological or any clinical features. Channel variants showed a consistent effect on channel deactivation, slowing the rate of channel closure following normal activation. This specific gain-of-function feature is likely to underlie the neurological phenotype in our patients. Our data highlight KCNA6 as a novel channelopathy gene associated with early infantile epileptic phenotypes and neurodevelopmental anomalies.
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Affiliation(s)
- Vincenzo Salpietro
- Department of Neuromuscular DiseaseUCL Institute of Neurology, University College LondonLondonUK
- Department of Biotechnological and Applied Clinical Sciences (DISCAB)University of L'AquilaL'AquilaItaly
| | | | - Stephanie Efthymiou
- Department of Neuromuscular DiseaseUCL Institute of Neurology, University College LondonLondonUK
| | - Emer O'Connor
- Department of Neuromuscular DiseaseUCL Institute of Neurology, University College LondonLondonUK
| | - Anna Marcé‐Grau
- Department of Paediatric Neurology, University Hospital Vall d'HebronUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Reza Maroofian
- Department of Neuromuscular DiseaseUCL Institute of Neurology, University College LondonLondonUK
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI)University of Genoa16124 GenoaItaly
- Unit of Pediatric NeurologyIRCCS, Istituto “Giannina Gaslini”Genoa 16123Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI)University of Genoa16124 GenoaItaly
- Medical Genetics UnitIRCCS, Istituto “Giannina Gaslini”Genoa 16123Italy
| | | | | | | | | | - Júlia Sala‐Coromina
- Department of Paediatric Neurology, University Hospital Vall d'HebronUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI)University of Genoa16124 GenoaItaly
- Medical Genetics UnitIRCCS, Istituto “Giannina Gaslini”Genoa 16123Italy
| | | | - Marie Alesandrini
- Neuropediatrics UnitCentre Hospitalier Universitaire NantesNantesFrance
| | - P. Y. Billie Au
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of MedicineUniversity of CalgaryAlbertaCalgaryCanada
| | - Nilika Shah Singhal
- Departments of Neurology and Pediatrics, UCSF Benioff Children's HospitalUniversity of CaliforniaCaliforniaSan FranciscoUSA
| | - Benjamin Cogne
- Centre Hospitalier Universitaire NantesService de Génétique MédicaleNantesFrance
- Université de Nantes, CNRS, INSERML'Institut du ThoraxNantesFrance
| | - Bertrand Isidor
- Centre Hospitalier Universitaire NantesService de Génétique MédicaleNantesFrance
- Université de Nantes, CNRS, INSERML'Institut du ThoraxNantesFrance
| | - Michael G. Hanna
- Department of Neuromuscular DiseaseUCL Institute of Neurology, University College LondonLondonUK
- Queen Square Centre for Neuromuscular DiseasesNational Hospital for Neurology and NeurosurgeryLondonUK
| | - Alfons Macaya
- Department of Paediatric Neurology, University Hospital Vall d'HebronUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Dimitri M. Kullmann
- Department of Clinical and Experimental EpilepsyUCL Institute of Neurology, University College LondonLondonUK
| | - Henry Houlden
- Department of Neuromuscular DiseaseUCL Institute of Neurology, University College LondonLondonUK
| | - Roope Männikkö
- Department of Neuromuscular DiseaseUCL Institute of Neurology, University College LondonLondonUK
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Alijanpour S, Miryounesi M, Ghafouri-Fard S. The role of excitatory amino acid transporter 2 (EAAT2) in epilepsy and other neurological disorders. Metab Brain Dis 2023; 38:1-16. [PMID: 36173507 DOI: 10.1007/s11011-022-01091-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/15/2022] [Indexed: 02/03/2023]
Abstract
Glutamate is the major excitatory neurotransmitter in the central nervous system (CNS). Excitatory amino acid transporters (EAATs) have important roles in the uptake of glutamate and termination of glutamatergic transmission. Up to now, five EAAT isoforms (EAAT1-5) have been identified in mammals. The main focus of this review is EAAT2. This protein has an important role in the pathoetiology of epilepsy. De novo dominant mutations, as well as inherited recessive mutation in this gene, have been associated with epilepsy. Moreover, dysregulation of this protein is implicated in a range of neurological diseases, namely amyotrophic lateral sclerosis, alzheimer's disease, parkinson's disease, schizophrenia, epilepsy, and autism. In this review, we summarize the role of EAAT2 in epilepsy and other neurological disorders, then provide an overview of the therapeutic modulation of this protein.
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Affiliation(s)
- Sahar Alijanpour
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Miryounesi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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4
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Alam A, Parfyonov M, Huang CY, Gill I, Connolly MB, Illes J. Targeted Whole Exome Sequencing in Children With Early-Onset Epilepsy: Parent Experiences. J Child Neurol 2022; 37:840-850. [PMID: 35921196 PMCID: PMC9554160 DOI: 10.1177/08830738221113901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study investigated the experiences of 25 caregivers of children with early-onset, treatment-resistant epilepsy who pursued whole exome sequencing to determine the impact of the test results on their child's treatment. Caregivers who consented to be recontacted were recruited from a previous study investigating the diagnostic yield of whole exome sequencing. A semistructured interview addressed questions based on one of 2 study phases. The first phase discussed the decision-making process for genetic testing (15 interviews), which revealed 4 major themes: (1) prognosis, (2) engagement, (3) concerns, and (4) autonomy. The second phase discussed the impact of genetic testing on treatment (10 interviews), which revealed 3 major themes: (1) testing features, (2) emotional impact, and (3) treatment outcomes. Overall, parents pursued genetic testing to obtain a clear prognosis, inform treatment decisions, engage with other families, and exercise autonomy. Caregivers felt that early testing is warranted to inform their child's diagnostic odyssey.
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Affiliation(s)
- Armaghan Alam
- Neuroethics Canada, Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Maksim Parfyonov
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Department of Pediatrics, Division of Neurology, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Camille Y. Huang
- Neuroethics Canada, Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Inderpal Gill
- Department of Pediatrics, Division of Neurology, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Mary B. Connolly
- Department of Pediatrics, Division of Neurology, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Judy Illes
- Neuroethics Canada, Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Judy Illes, CM, PhD, Professor of Neurology, Department of Medicine, University of British Columbia, 2211 Wesbrook Mall, Koerner S124, Vancouver, BC V6T 2B5 Canada.
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5
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Sun H, Shen XR, Fang ZB, Jiang ZZ, Wei XJ, Wang ZY, Yu XF. Next-Generation Sequencing Technologies and Neurogenetic Diseases. Life (Basel) 2021; 11:life11040361. [PMID: 33921670 PMCID: PMC8072598 DOI: 10.3390/life11040361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/05/2021] [Accepted: 04/16/2021] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing (NGS) technology has led to great advances in understanding the causes of Mendelian and complex neurological diseases. Owing to the complexity of genetic diseases, the genetic factors contributing to many rare and common neurological diseases remain poorly understood. Selecting the correct genetic test based on cost-effectiveness, coverage area, and sequencing range can improve diagnosis, treatments, and prevention. Whole-exome sequencing and whole-genome sequencing are suitable methods for finding new mutations, and gene panels are suitable for exploring the roles of specific genes in neurogenetic diseases. Here, we provide an overview of the classifications, applications, advantages, and limitations of NGS in research on neurological diseases. We further provide examples of NGS-based explorations and insights of the genetic causes of neurogenetic diseases, including Charcot-Marie-Tooth disease, spinocerebellar ataxias, epilepsy, and multiple sclerosis. In addition, we focus on issues related to NGS-based analyses, including interpretations of variants of uncertain significance, de novo mutations, congenital genetic diseases with complex phenotypes, and single-molecule real-time approaches.
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Affiliation(s)
| | | | | | | | | | | | - Xue-Fan Yu
- Correspondence: ; Tel.: +86-157-5430-1836
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6
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Deep phenotyping unstructured data mining in an extensive pediatric database to unravel a common KCNA2 variant in neurodevelopmental syndromes. Genet Med 2021; 23:968-971. [PMID: 33500571 PMCID: PMC8105164 DOI: 10.1038/s41436-020-01039-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023] Open
Abstract
Purpose Electronic health records are gaining popularity to detect and propose interdisciplinary treatments for patients with similar medical histories, diagnoses, and outcomes. These files are compiled by different nonexperts and expert clinicians. Data mining in these unstructured data is a transposable and sustainable methodology to search for patients presenting a high similitude of clinical features. Methods Exome and targeted next-generation sequencing bioinformatics analyses were performed at the Imagine Institute. Similarity Index (SI), an algorithm based on a vector space model (VSM) that exploits concepts extracted from clinical narrative reports was used to identify patients with highly similar clinical features. Results Here we describe a case of “automated diagnosis” indicated by Dr. Warehouse, a biomedical data warehouse oriented toward clinical narrative reports, developed at Necker Children’s Hospital using around 500,000 patients’ records. Through the use of this warehouse, we were able to match and identify two patients sharing very specific clinical neonatal and childhood features harboring the same de novo variant in KCNA2. Conclusion This innovative application of database clustering clinical features could advance identification of patients with rare and common genetic conditions and detect with high accuracy the natural history of patients harboring similar genetic pathogenic variants.
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7
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Karayağmurlu A, Dursun OB, Esin İS, Coşkun M. Serum NGF levels may be associated with intrauterine antiepileptic exposure-related developmental problems. Epilepsy Behav 2019; 97:60-66. [PMID: 31181430 DOI: 10.1016/j.yebeh.2019.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 01/16/2023]
Abstract
OBJECTIVE It has been shown that maternal epilepsy and antiepileptic drug use during pregnancy have adverse developmental outcomes in children. The aim of this study was to investigate the developmental outcomes of maternal epilepsy and prenatal antiepileptic exposure. We also looked for the associations between serum levels of glial cell-derived neurotrophic factor (GDNF) and nerve growth factor (NGF) and developmental outcomes. METHODS This is a retrospective, nonrandomized, case-controlled study. Fifty-three children aged two to six years old with maternal epilepsy were included in the case group. Fifty-three age- and gender-matched children without maternal epilepsy were included in the control group. Developmental assessment was conducted using the Denver II Developmental Screening Test (DDST-II). Serum levels of NGF and GDNF were measured using an enzyme-linked immunosorbent assay (ELISA) kit. RESULTS Multiple regression analysis revealed that prenatal antiepileptic exposure was significantly associated with lower global developmental scores (B = -7.5, confidence interval (CI): -13.1; -1.9, p = 0.009) while periconceptional folate use was associated with a reduced risk for adverse developmental outcomes (B = 6.6, CI: 0.91; 12.3, p = 0.024). Children with prenatal antiepileptic exposure are at increased risk for global developmental delay (GDD) particularly for language domain (p = 0.018). We found a statistically significant positive correlation between NGF levels and global developmental scores (r = 0.302, p = 0.009). Serum levels of GDNF in children with maternal epilepsy were significantly lower than the children without maternal epilepsy (p = 0.025). CONCLUSIONS Prenatal antiepileptic exposure was related with the increased risk of GDD while periconceptional folate use was related with lower risk. Clinicians should inform all women in reproductive age with epilepsy about the possible benefits and risks of antiepileptic drug use during a possible pregnancy. Periconceptional folate use has protective effect on child development, and all women on antiepileptic drugs should be encouraged for periconceptional folate use. Serum NGF levels may be a promising biomarker for monitoring global development delay in at-risk population.
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Affiliation(s)
- Ali Karayağmurlu
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Istanbul University, İstanbul, Turkey.
| | - Onur Burak Dursun
- Department of Child and Adolescent Psychiatry, University of Health Sciences, International School of Medicine, Istanbul, Turkey
| | - İbrahim Selçuk Esin
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Murat Coşkun
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, Istanbul University, İstanbul, Turkey
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8
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Pippucci T, Licchetta L, Baldassari S, Marconi C, De Luise M, Myers C, Nardi E, Provini F, Cameli C, Minardi R, Bacchelli E, Giordano L, Crichiutti G, d'Orsi G, Seri M, Gasparre G, Mefford HC, Tinuper P, Bisulli F. Contribution of ultrarare variants in mTOR pathway genes to sporadic focal epilepsies. Ann Clin Transl Neurol 2019; 6:475-485. [PMID: 30911571 PMCID: PMC6414475 DOI: 10.1002/acn3.722] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 01/16/2023] Open
Abstract
Objective We investigated the contribution to sporadic focal epilepsies (FE) of ultrarare variants in genes coding for the components of complexes regulating mechanistic Target Of Rapamycin (mTOR)complex 1 (mTORC1). Methods We collected genetic data of 121 Italian isolated FE cases and 512 controls by Whole Exome Sequencing (WES) and single‐molecule Molecular Inversion Probes (smMIPs) targeting 10 genes of the GATOR1, GATOR2, and TSC complexes. We collapsed “qualifying” variants (ultrarare and predicted to be deleterious or loss of function) across the examined genes and sought to identify their enrichment in cases compared to controls. Results We found eight qualifying variants in cases and nine in controls, demonstrating enrichment in FE patients (P = 0.006; exact unconditional test, one‐tailed). Pathogenic variants were identified in DEPDC5 and TSC2, both major genes for Mendelian FE syndromes. Interpretation Our findings support the contribution of ultrarare variants in genes in the mTOR pathway complexes GATOR and TSC to the risk of sporadic FE and a shared genetic basis between rare and common epilepsies. The identification of a monogenic etiology in isolated cases, most typically encountered in clinical practice, may offer to a broader community of patients the perspective of precision therapies directed by the underlying genetic cause.
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Affiliation(s)
- Tommaso Pippucci
- Medical Genetics Unit Polyclinic Sant'Orsola-Malpighi University Hospital Bologna Italy
| | - Laura Licchetta
- IRCCS Istituto delle Scienze Neurologiche di Bologna Bologna Italy.,Department of Biomedical and Neuromotor Sciences (DIBINEM) University of Bologna Bologna Italy
| | - Sara Baldassari
- Department of Biomedical and Surgical Sciences (DIMEC) University of Bologna Bologna Italy
| | - Caterina Marconi
- Department of Biomedical and Surgical Sciences (DIMEC) University of Bologna Bologna Italy
| | - Monica De Luise
- Department of Biomedical and Surgical Sciences (DIMEC) University of Bologna Bologna Italy
| | - Candace Myers
- Division of Genetic Medicine Department of Pediatrics University of Washington Seattle Washington
| | - Elena Nardi
- Department of Statistical Sciences "Paolo Fortunati" University of Bologna Bologna Italy
| | - Federica Provini
- IRCCS Istituto delle Scienze Neurologiche di Bologna Bologna Italy.,Department of Biomedical and Neuromotor Sciences (DIBINEM) University of Bologna Bologna Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology University of Bologna Bologna Italy
| | - Raffaella Minardi
- IRCCS Istituto delle Scienze Neurologiche di Bologna Bologna Italy.,Department of Biomedical and Neuromotor Sciences (DIBINEM) University of Bologna Bologna Italy
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology University of Bologna Bologna Italy
| | - Lucio Giordano
- Neuropsychiatric Department Spedali Civili Brescia Italy
| | - Giovanni Crichiutti
- Division of Pediatrics Department of Medicine University of Udine Udine Italy
| | - Giuseppe d'Orsi
- Epilepsy Center Clinic of Nervous System Diseases University of Foggia Riuniti Hospital Foggia Italy
| | - Marco Seri
- Medical Genetics Unit Polyclinic Sant'Orsola-Malpighi University Hospital Bologna Italy.,Department of Biomedical and Surgical Sciences (DIMEC) University of Bologna Bologna Italy
| | - Giuseppe Gasparre
- Department of Biomedical and Surgical Sciences (DIMEC) University of Bologna Bologna Italy
| | - Heather C Mefford
- Division of Genetic Medicine Department of Pediatrics University of Washington Seattle Washington
| | - Paolo Tinuper
- IRCCS Istituto delle Scienze Neurologiche di Bologna Bologna Italy.,Department of Biomedical and Neuromotor Sciences (DIBINEM) University of Bologna Bologna Italy
| | - Francesca Bisulli
- IRCCS Istituto delle Scienze Neurologiche di Bologna Bologna Italy.,Department of Biomedical and Neuromotor Sciences (DIBINEM) University of Bologna Bologna Italy
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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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10
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Tran Mau-Them F, Guibaud L, Duplomb L, Keren B, Lindstrom K, Marey I, Mochel F, van den Boogaard MJ, Oegema R, Nava C, Masurel A, Jouan T, Jansen FE, Au M, Chen AH, Cho M, Duffourd Y, Lozier E, Konovalov F, Sharkov A, Korostelev S, Urteaga B, Dickson P, Vera M, Martínez-Agosto JA, Begemann A, Zweier M, Schmitt-Mechelke T, Rauch A, Philippe C, van Gassen K, Nelson S, Graham JM, Friedman J, Faivre L, Lin HJ, Thauvin-Robinet C, Vitobello A. De novo truncating variants in the intronless IRF2BPL are responsible for developmental epileptic encephalopathy. Genet Med 2018; 21:1008-1014. [DOI: 10.1038/s41436-018-0143-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023] Open
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11
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Balestrini S, Sisodiya SM. Personalized treatment in the epilepsies: challenges and opportunities. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1486189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Simona Balestrini
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, and Epilepsy Society, Chalfont-St-Peter, Bucks, United Kingdom
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, and Epilepsy Society, Chalfont-St-Peter, Bucks, United Kingdom
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12
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A Recurrent De Novo PACS2 Heterozygous Missense Variant Causes Neonatal-Onset Developmental Epileptic Encephalopathy, Facial Dysmorphism, and Cerebellar Dysgenesis. Am J Hum Genet 2018; 102:995-1007. [PMID: 29656858 DOI: 10.1016/j.ajhg.2018.03.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/27/2018] [Indexed: 11/24/2022] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) represent a large clinical and genetic heterogeneous group of neurodevelopmental diseases. The identification of pathogenic genetic variants in DEEs remains crucial for deciphering this complex group and for accurately caring for affected individuals (clinical diagnosis, genetic counseling, impacting medical, precision therapy, clinical trials, etc.). Whole-exome sequencing and intensive data sharing identified a recurrent de novo PACS2 heterozygous missense variant in 14 unrelated individuals. Their phenotype was characterized by epilepsy, global developmental delay with or without autism, common cerebellar dysgenesis, and facial dysmorphism. Mixed focal and generalized epilepsy occurred in the neonatal period, controlled with difficulty in the first year, but many improved in early childhood. PACS2 is an important PACS1 paralog and encodes a multifunctional sorting protein involved in nuclear gene expression and pathway traffic regulation. Both proteins harbor cargo(furin)-binding regions (FBRs) that bind cargo proteins, sorting adaptors, and cellular kinase. Compared to the defined PACS1 recurrent variant series, individuals with PACS2 variant have more consistently neonatal/early-infantile-onset epilepsy that can be challenging to control. Cerebellar abnormalities may be similar but PACS2 individuals exhibit a pattern of clear dysgenesis ranging from mild to severe. Functional studies demonstrated that the PACS2 recurrent variant reduces the ability of the predicted autoregulatory domain to modulate the interaction between the PACS2 FBR and client proteins, which may disturb cellular function. These findings support the causality of this recurrent de novo PACS2 heterozygous missense in DEEs with facial dysmorphim and cerebellar dysgenesis.
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Lindy AS, Stosser MB, Butler E, Downtain‐Pickersgill C, Shanmugham A, Retterer K, Brandt T, Richard G, McKnight DA. Diagnostic outcomes for genetic testing of 70 genes in 8565 patients with epilepsy and neurodevelopmental disorders. Epilepsia 2018; 59:1062-1071. [DOI: 10.1111/epi.14074] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2018] [Indexed: 12/16/2022]
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Yu Y, Hasegawa D, Fujiwara-Igarashi A, Hamamoto Y, Mizoguchi S, Kuwabara T, Fujita M. Molecular cloning and characterization of the family of feline leucine-rich glioma-inactivated (LGI) genes, and mutational analysis in familial spontaneous epileptic cats. BMC Vet Res 2017; 13:389. [PMID: 29237452 PMCID: PMC5729232 DOI: 10.1186/s12917-017-1308-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/28/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leucine-rich glioma-inactivated (LGI) proteins play a critical role in synaptic transmission. Dysfunction of these genes and encoded proteins is associated with neurological disorders such as genetic epilepsy or autoimmune limbic encephalitis in animals and human. Familial spontaneous epileptic cats (FSECs) are the only feline strain and animal model of familial temporal lobe epilepsy. The seizure semiology of FSECs comprises recurrent limbic seizures with or without evolution into generalized epileptic seizures, while cats with antibodies against voltage-gated potassium channel complexed/LGI1 show limbic encephalitis and recurrent limbic seizures. However, it remains unclear whether the genetics underlying FSECs are associated with LGI family genes. In the present study, we cloned and characterized the feline LGI1-4 genes and examined their association with FSECs. Conventional PCR techniques were performed for cloning and mutational analysis. Characterization was predicted using bioinformatics software. RESULTS The cDNAs of feline LGI1-4 contained 1674-bp, 1650-bp, 1647-bp, and 1617-bp open reading frames, respectively, and encoded proteins comprising 557, 549, 548, and 538 amino acid residues, respectively. The feline LGI1-4 putative protein sequences showed high homology with Homo sapiens, Canis familiaris, Bos taurus, Sus scrofa, and Equus caballus (92%-100%). Mutational analysis in 8 FSECs and 8 controls for LGI family genes revealed 3 non-synonymous and 14 synonymous single nucleotide polymorphisms in the coding region. Only one non-synonymous single nucleotide polymorphism in LGI4 was found in 3 out of 8 FSECs. Using three separate computational tools, this mutation was not predicted to be disease causing. No co-segregation of the disease was found with any variant. CONCLUSIONS We cloned the cDNAs of the four feline LGI genes, analyzed the amino acid sequences, and revealed that epilepsy in FSEC is not a monogenic disorder associated with LGI genes.
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Affiliation(s)
- Yoshihiko Yu
- Department of Clinical Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan.
| | - Daisuke Hasegawa
- Department of Clinical Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan.
| | - Aki Fujiwara-Igarashi
- Department of Clinical Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Yuji Hamamoto
- Department of Clinical Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Shunta Mizoguchi
- Department of Clinical Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Takayuki Kuwabara
- Department of Clinical Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Michio Fujita
- Department of Clinical Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
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Payne K, Eden M, Davison N, Bakker E. Toward health technology assessment of whole-genome sequencing diagnostic tests: challenges and solutions. Per Med 2017; 14:235-247. [PMID: 29767583 DOI: 10.2217/pme-2016-0089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Whole-genome sequencing (WGS) is being applied within research settings across Europe to develop genomic WGS-based diagnostic tests. The focus of this perspective paper is to describe if, and how, current approaches of health technology assessment could be applied to WGS-based diagnostic tests. This perspective draws on the collective view from a trans-European multidisciplinary consortium of methodologists, clinicians and scientists. Specific challenges can be described by using the PICO (population, intervention, comparator, outcome) framework to inform health technology assessment. Practical solutions are suggested which require joined-up, multidisciplinary working across healthcare systems using existing expert networks so that emergent issues for the health technology assessment of WGS can be met in a timely fashion.
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Affiliation(s)
- Katherine Payne
- Manchester Centre for Health Economics, The University of Manchester, Manchester M13 9PL, UK
| | - Martin Eden
- Manchester Centre for Health Economics, The University of Manchester, Manchester M13 9PL, UK
| | - Niall Davison
- Manchester Centre for Health Economics, The University of Manchester, Manchester M13 9PL, UK
| | - Egbert Bakker
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Unexplained Early Infantile Epileptic Encephalopathy in Han Chinese Children: Next-Generation Sequencing and Phenotype Enriching. Sci Rep 2017; 7:46227. [PMID: 28387369 PMCID: PMC5384237 DOI: 10.1038/srep46227] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/13/2017] [Indexed: 11/08/2022] Open
Abstract
Early Infantile Epileptic Encephalopathy (EIEE) presents shortly after birth with frequent, severe seizures and progressive disturbance of cerebral function. This study was to investigate a cohort of Chinese children with unexplained EIEE, infants with previous genetic diagnoses, causative brain malformations, or inborn errors of metabolism were excluded. We used targeted next-generation sequencing to identify potential pathogenic variants of 308 genes in 68 Han Chinese patients with unexplained EIEE. A filter process was performed to prioritize rare variants of potential functional significance. In all cases where parental testing was accessible, Sanger sequencing confirmed the variants and determined the parental origin. In 15% of patients (n = 10/68), we identified nine de novo pathogenic variants, and one assumed de novo pathogenic variant in the following genes: CDKL5 (n = 2), STXBP1 (n = 2), SCN1A (n = 3), KCNQ2 (n = 2), SCN8A (n = 1), four of the variants are novel variants. In 4% patients (n = 3/68), we identified three likely pathogenic variants; two assumed de novo and one X-linked in the following genes: SCN1A (n = 2) and ARX (n = 1), two of these variants are novel. Variants were assumed de novo when parental testing was not available. Our findings were first reported in Han Chinese patients with unexplained EIEE, enriching the EIEE mutation spectrum bank.
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Alhusaini S, Whelan CD, Sisodiya SM, Thompson PM. Quantitative magnetic resonance imaging traits as endophenotypes for genetic mapping in epilepsy. NEUROIMAGE-CLINICAL 2016; 12:526-534. [PMID: 27672556 PMCID: PMC5030372 DOI: 10.1016/j.nicl.2016.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/21/2016] [Accepted: 09/05/2016] [Indexed: 12/18/2022]
Abstract
Over the last decade, the field of imaging genomics has combined high-throughput genotype data with quantitative magnetic resonance imaging (QMRI) measures to identify genes associated with brain structure, cognition, and several brain-related disorders. Despite its successful application in different psychiatric and neurological disorders, the field has yet to be advanced in epilepsy. In this article we examine the relevance of imaging genomics for future genetic studies in epilepsy from three perspectives. First, we discuss prior genome-wide genetic mapping efforts in epilepsy, considering the possibility that some studies may have been constrained by inherent theoretical and methodological limitations of the genome-wide association study (GWAS) method. Second, we offer a brief overview of the imaging genomics paradigm, from its original inception, to its role in the discovery of important risk genes in a number of brain-related disorders, and its successful application in large-scale multinational research networks. Third, we provide a comprehensive review of past studies that have explored the eligibility of brain QMRI traits as endophenotypes for epilepsy. While the breadth of studies exploring QMRI-derived endophenotypes in epilepsy remains narrow, robust syndrome-specific neuroanatomical QMRI traits have the potential to serve as accessible and relevant intermediate phenotypes for future genetic mapping efforts in epilepsy. QMRI traits have the potential to serve as robust intermediate phenotypes for brain-related disorders. Hippocampal volume is the most promising neuroimaging endophenotype for MTLE + HS. Imaging genomics holds great promise in advancing epilepsy genetic research. Studies are encouraged to explore the validity of QMRI traits as endophenotypes for epilepsy.
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Affiliation(s)
- Saud Alhusaini
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Christopher D Whelan
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Hospitals Biomedical Research Centre, UCL Institute of Neurology, London, UK
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
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18
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Dos Passos GR, Fernández AC, Vasques AM, Martins WA, Palmini A. Mother and daughter with adolescent-onset severe frontal lobe dysfunction and epilepsy. Dement Neuropsychol 2016; 10:238-243. [PMID: 29213461 PMCID: PMC5642421 DOI: 10.1590/s1980-5764-2016dn1003011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Familial cases of early-onset prominent frontal lobe dysfunction associated with
epilepsy have not been reported to date. We report a mother and her only daughter
with incapacitating behavioral manifestations of frontal lobe dysfunction and
epilepsy of variable severity. The possibility of a hitherto undescribed genetic
condition is discussed.
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Affiliation(s)
| | - Alonso Cuadrado Fernández
- Neurology Service, São Lucas Hospital, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre RS, Brazil
| | - Adriana Machado Vasques
- Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul, RS, Porto Alegre, Brazil
| | - William Alves Martins
- Neurology Service, São Lucas Hospital, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre RS, Brazil.,Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul, RS, Porto Alegre, Brazil
| | - André Palmini
- Neurology Service, São Lucas Hospital, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre RS, Brazil.,Porto Alegre Epilepsy Surgery Program, Neurology Service, São Lucas Hospital, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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Becherucci F, Mazzinghi B, Provenzano A, Murer L, Giglio S, Romagnani P. Lessons from genetics: is it time to revise the therapeutic approach to children with steroid-resistant nephrotic syndrome? J Nephrol 2016; 29:543-50. [DOI: 10.1007/s40620-016-0315-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/29/2016] [Indexed: 11/30/2022]
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