1
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Dwivedi R, Kaushik M, Tripathi M, Dada R, Tiwari P. Unraveling the genetic basis of epilepsy: Recent advances and implications for diagnosis and treatment. Brain Res 2024; 1843:149120. [PMID: 39032529 DOI: 10.1016/j.brainres.2024.149120] [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: 05/20/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024]
Abstract
Epilepsy, affecting approximately 1% of the global population, manifests as recurring seizures and is heavily influenced by genetic factors. Recent advancements in genetic technologies have revolutionized our understanding of epilepsy's genetic landscape. Key studies, such as the discovery of mutations in ion channels (e.g., SCN1A and SCN2A), neurotransmitter receptors (e.g., GABRA1), and synaptic proteins (e.g., SYNGAP1, KCNQ2), have illuminated critical pathways underlying epilepsy susceptibility and pathogenesis. Genome-wide association studies (GWAS) have identified specific genetic variations linked to epilepsy risk, such as variants near SCN1A and PCDH7, enhancing diagnostic accuracy and enabling personalized treatment strategies. Moreover, epigenetic mechanisms, including DNA methylation (e.g., MBD5), histone modifications (e.g., HDACs), and non-coding RNAs (e.g., miR-134), play pivotal roles in altering gene expression and synaptic plasticity, contributing to epileptogenesis. These discoveries offer promising avenues for therapeutic interventions aimed at improving outcomes for epilepsy patients. Genetic testing has become essential in clinical practice, facilitating precise diagnosis and tailored management approaches based on individual genetic profiles. Furthermore, insights into epigenetic regulation suggest novel therapeutic targets for developing more effective epilepsy treatments. In summary, this review highlights significant progress in understanding the genetic and epigenetic foundations of epilepsy. By integrating findings from key studies and specifying genes involved in epigenetic modifications, we underscore the potential for advanced therapeutic strategies in this complex neurological disorder, emphasizing the importance of personalized medicine approaches in epilepsy management.
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Affiliation(s)
- Rekha Dwivedi
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Meenakshi Kaushik
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Manjari Tripathi
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Rima Dada
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Prabhakar Tiwari
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India.
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2
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Cheng M, Bai L, Yang Y, Liu W, Niu X, Chen Y, Tan Q, Yang X, Wu Q, Zhao HQ, Zhang Y. Novel copy number variations and phenotypes of infantile epileptic spasms syndrome. Clin Genet 2024; 106:161-179. [PMID: 38544467 DOI: 10.1111/cge.14520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 07/02/2024]
Abstract
We summarize the copy number variations (CNVs) and phenotype spectrum of infantile epileptic spasms syndrome (IESS) in a Chinese cohort. The CNVs were identified by genomic copy number variation sequencing. The CNVs and clinical data were analyzed. 74 IESS children with CNVs were enrolled. 35 kinds of CNVs were identified. There were 11 deletions and 5 duplications not reported previously in IESS, including 2 CNVs not reported in epilepsy. 87.8% were de novo, 9.5% were inherited from mother and 2.7% from father. Mosaicism occurred in one patient with Xq21.31q25 duplication. 16.2% (12/74) were 1p36 deletion, and 20.3% (15/74) were 15q11-q13 duplication. The age of seizure onset ranged from 17 days to 24 months. Seizure types included epileptic spasms, focal seizures, tonic seizures, and myoclonic seizures. All patients displayed developmental delay. Additional features included craniofacial anomaly, microcephaly, congenital heart defects, and hemangioma. 29.7% of patients were seizure-free for more than 12 months, and 70.3% still had seizures after trying 2 or more anti-seizure medications. In conclusion, CNVs is a prominent etiology of IESS. 1p36 deletion and 15q duplication occurred most frequently. CNV detection should be performed in patients with IESS of unknown causes, especially in children with craniofacial anomalies and microcephaly.
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Affiliation(s)
- Miaomiao Cheng
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ling Bai
- Research and Development Center, Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Ying Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Wenwei Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xueyang Niu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yi Chen
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Quanzhen Tan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Qixi Wu
- Research and Development Center, Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Han-Qing Zhao
- Research and Development Center, Beijing USCI Medical Laboratory Co., Ltd, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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3
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Montanucci L, Lewis-Smith D, Collins RL, Niestroj LM, Parthasarathy S, Xian J, Ganesan S, Macnee M, Brünger T, Thomas RH, Talkowski M, Helbig I, Leu C, Lal D. Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals. Nat Commun 2023; 14:4392. [PMID: 37474567 PMCID: PMC10359300 DOI: 10.1038/s41467-023-39539-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/16/2023] [Indexed: 07/22/2023] Open
Abstract
Copy number variants (CNV) are established risk factors for neurodevelopmental disorders with seizures or epilepsy. With the hypothesis that seizure disorders share genetic risk factors, we pooled CNV data from 10,590 individuals with seizure disorders, 16,109 individuals with clinically validated epilepsy, and 492,324 population controls and identified 25 genome-wide significant loci, 22 of which are novel for seizure disorders, such as deletions at 1p36.33, 1q44, 2p21-p16.3, 3q29, 8p23.3-p23.2, 9p24.3, 10q26.3, 15q11.2, 15q12-q13.1, 16p12.2, 17q21.31, duplications at 2q13, 9q34.3, 16p13.3, 17q12, 19p13.3, 20q13.33, and reciprocal CNVs at 16p11.2, and 22q11.21. Using genetic data from additional 248,751 individuals with 23 neuropsychiatric phenotypes, we explored the pleiotropy of these 25 loci. Finally, in a subset of individuals with epilepsy and detailed clinical data available, we performed phenome-wide association analyses between individual CNVs and clinical annotations categorized through the Human Phenotype Ontology (HPO). For six CNVs, we identified 19 significant associations with specific HPO terms and generated, for all CNVs, phenotype signatures across 17 clinical categories relevant for epileptologists. This is the most comprehensive investigation of CNVs in epilepsy and related seizure disorders, with potential implications for clinical practice.
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Affiliation(s)
- Ludovica Montanucci
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, USA
| | - David Lewis-Smith
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Clinical Neurosciences, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.) and Harvard, Cambridge, USA
| | | | - Shridhar Parthasarathy
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Julie Xian
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiva Ganesan
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie Macnee
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Tobias Brünger
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Rhys H Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Clinical Neurosciences, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michael Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.) and Harvard, Cambridge, USA
| | - Ingo Helbig
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, USA.
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, USA.
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, US.
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, USA.
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.) and Harvard, Cambridge, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, USA.
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, US.
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Hu H, Huang Y, Hou R, Xu H, Liu Y, Liao X, Xu J, Jiang L, Wang D. Xp22.31 copy number variations in 87 fetuses: refined genotype-phenotype correlations by prenatal and postnatal follow-up. BMC Med Genomics 2023; 16:69. [PMID: 37013593 PMCID: PMC10069036 DOI: 10.1186/s12920-023-01493-z] [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: 08/17/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Xp22.31 deletion and duplication have been described in various studies, but different laboratories interpret pathogenicity differently. OBJECTIVES Our study aimed to refine the genotype-phenotype associations between Xp22.31 copy number variants in fetuses, with the aim of providing data support to genetic counseling. METHODS We retrospectively analyzed karyotyping and single nucleotide polymorphism array results from 87 fetuses and their family members. Phenotypic data were obtained through follow-up visits. RESULTS The percentage of fetuses carrying the Xp22.31 deletions (9 females, 12 males) was 24.1% (n = 21), while duplications (38 females, 28 males) accounted for 75.9% (n = 66). Here, we noted that the typical region (from 6.4 to 8.1 Mb, hg19) was detected in the highest ratio, either in the fetuses with deletions (76.2%, 16 of 21) or duplications (69.7%, 46 of 66). In female deletion carriers, termination of pregnancy was chosen for two fetuses, and the remaining seven were born without distinct phenotypic abnormalities. In male deletion carriers, termination of pregnancy was chosen for four fetuses, and the remaining eight of them displayed ichthyosis without neurodevelopmental anomalies. In two of these cases, the chromosomal imbalance was inherited from the maternal grandfathers, who also only had ichthyosis phenotypes. Among the 66 duplication carriers, two cases were lost at follow-up, and pregnancy was terminated for eight cases. There were no other clinical findings in the rest of the 56 fetuses, including two with Xp22.31 tetrasomy, for either male or female carriers. CONCLUSION Our observations provide support for genetic counseling in male and female carriers of Xp22.31 copy number variants. Most of them are asymptomatic in male deletion carriers, except for skin findings. Our study is consistent with the view that the Xp22.31 duplication may be a benign variant in both sexes.
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Affiliation(s)
- Huamei Hu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yulin Huang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Renke Hou
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Huanhuan Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yalan Liu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xueqian Liao
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Juchun Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Lupin Jiang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
| | - Dan Wang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
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5
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Brownstein CA, Douard E, Haynes RL, Koh HY, Haghighi A, Keywan C, Martin B, Alexandrescu S, Haas EA, Vargas SO, Wojcik MH, Jacquemont S, Poduri AH, Goldstein RD, Holm IA. Copy Number Variation and Structural Genomic Findings in 116 Cases of Sudden Unexplained Death between 1 and 28 Months of Age. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2200012. [PMID: 36910592 PMCID: PMC10000288 DOI: 10.1002/ggn2.202200012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/31/2022] [Indexed: 11/09/2022]
Abstract
In sudden unexplained death in pediatrics (SUDP) the cause of death is unknown despite an autopsy and investigation. The role of copy number variations (CNVs) in SUDP has not been well-studied. Chromosomal microarray (CMA) data are generated for 116 SUDP cases with age at death between 1 and 28 months. CNVs are classified using the American College of Medical Genetics and Genomics guidelines and CNVs in our cohort are compared to an autism spectrum disorder (ASD) cohort, and to a control cohort. Pathogenic CNVs are identified in 5 of 116 cases (4.3%). Variants of uncertain significance (VUS) favoring pathogenic CNVs are identified in 9 cases (7.8%). Several CNVs are associated with neurodevelopmental phenotypes including seizures, ASD, developmental delay, and schizophrenia. The structural variant 47,XXY is identified in two cases (2/69 boys, 2.9%) not previously diagnosed with Klinefelter syndrome. Pathogenicity scores for deletions are significantly elevated in the SUDP cohort versus controls (p = 0.007) and are not significantly different from the ASD cohort. The finding of pathogenic or VUS favoring pathogenic CNVs, or structural variants, in 12.1% of cases, combined with the observation of higher pathogenicity scores for deletions in SUDP versus controls, suggests that CMA should be included in the genetic evaluation of SUDP.
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6
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Moreau C, Tremblay F, Wolking S, Girard A, Laprise C, Hamdan FF, Michaud JL, Minassian BA, Cossette P, Girard SL. Assessment of burden and segregation profiles of CNVs in patients with epilepsy. Ann Clin Transl Neurol 2022; 9:1050-1058. [PMID: 35678011 PMCID: PMC9268881 DOI: 10.1002/acn3.51598] [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: 03/14/2022] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 11/12/2022] Open
Abstract
Objective Microdeletions are associated with different forms of epilepsy but show incomplete penetrance, which is not well understood. We aimed to assess whether unmasked variants or double CNVs could explain incomplete penetrance. Methods We analyzed copy number variants (CNVs) in 603 patients with four different subgroups of epilepsy and 945 controls. CNVs were called from genotypes and validated on whole‐genome (WGS) or whole‐exome sequences (WES). CNV burden difference between patients and controls was obtained by fitting a logistic regression. CNV burden was assessed for small and large (>1 Mb) deletions and duplications and for deletions overlapping different gene sets. Results Large deletions were enriched in genetic generalized epilepsies (GGE) compared to controls. We also found enrichment of deletions in epilepsy genes and hotspots for GGE. We did not find truncating or functional variants that could have been unmasked by the deletions. We observed a double CNV hit in two patients. One patient also carried a de novo deletion in the 22q11.2 hotspot. Interpretation We could corroborate previous findings of an enrichment of large microdeletions and deletions in epilepsy genes in GGE. We could also replicate that microdeletions show incomplete penetrance. However, we could not validate the hypothesis of unmasked variants nor the hypothesis of double CNVs to explain the incomplete penetrance. We found a de novo CNV on 22q11.2 that could be of interest. We also observed GGE families carrying a deletion on 15q13.3 hotspot that could be investigated in the Quebec founder population.
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Affiliation(s)
- Claudia Moreau
- Department of Fundamental Sciences, University of Quebec in Chicoutimi, Chicoutimi, Canada
| | - Frédérique Tremblay
- Department of Fundamental Sciences, University of Quebec in Chicoutimi, Chicoutimi, Canada
| | - Stefan Wolking
- Department of Neurology and Epileptology, University Hospital RWTH Aachen, Aachen, Germany
| | - Alexandre Girard
- Department of Fundamental Sciences, University of Quebec in Chicoutimi, Chicoutimi, Canada
| | - Catherine Laprise
- Department of Fundamental Sciences, University of Quebec in Chicoutimi, Chicoutimi, Canada
| | - Fadi F Hamdan
- CHU Sainte-Justine Research Center, Montreal, Canada.,Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Jacques L Michaud
- CHU Sainte-Justine Research Center, Montreal, Canada.,Department of Neurosciences and Department of Pediatrics, University of Montreal, Montreal, Canada
| | - Berge A Minassian
- Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Canada.,Department of Pediatrics, University of Texas Southwestern, Dallas, Texas, USA
| | - Patrick Cossette
- CHUM Research Center, Montreal, Canada.,Department of Neurosciences, University of Montreal, Montreal, Canada
| | - Simon L Girard
- Department of Fundamental Sciences, University of Quebec in Chicoutimi, Chicoutimi, Canada.,CERVO Research Center, Laval University, Quebec, Canada
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7
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Li Z, Wang Y, Li L, He H, Lin L, Pan M, Yang T, Liu Q. A bibliometric analysis of the cause of sudden unexplained death in forensic medicine: Research trends, hot spots and prospects. Comput Biol Med 2022; 144:105330. [DOI: 10.1016/j.compbiomed.2022.105330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 01/03/2023]
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8
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Özaltun MF, Geyik S, Yılmaz ŞG. Screening for Copy Number Variations of the 15q13.3 Hotspot in CHRNA7 Gene and Expression in Patients with Migraines. Curr Issues Mol Biol 2021; 43:1090-1113. [PMID: 34563047 PMCID: PMC8929100 DOI: 10.3390/cimb43020078] [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: 08/04/2021] [Revised: 08/24/2021] [Accepted: 09/02/2021] [Indexed: 12/02/2022] Open
Abstract
Background: a migraine is a neurological disease. Copy number variation (CNV) is a phenomenon in which parts of the genome are repeated. We investigated the effects of the CNV and gene expression at the location 15q13.3 in the Cholinergic Receptor Nicotinic Alpha 7 Subunit (CHRNA7) gene, which we believe to be effective in the migraine clinic. Methods: we evaluated changes in CHRNA7 gene expression levels and CNV of 15q13.3 in patients with migraine (n = 102, with aura, n = 43; without aura, n = 59) according to healthy controls (n = 120) by q-PCR. The data obtained were analyzed against the reference telomerase reverse transcriptase (TERT) gene with the double copy number by standard curve analysis. Copy numbers were graded as a normal copy (2), gain (2>), and loss (<2). Results: we analyzed using the 2−ΔΔCT calculation method. The CHRNA7 gene was significantly downregulated in patients (p < 0.05). The analysis of CNV in the CHRNA7 gene was statistically significant in the patient group, according to healthy controls (p < 0.05). A decreased copy number indicates a dosage loss. However, no significant difference was observed among gain, normal, and loss copy numbers and expression values in patients (p > 0.05). The change in CNV was not associated with the downregulation of the CHRNA7 gene. Conclusion: Downregulation of the CHRNA7 gene may contribute to the formation of migraine by inactivation of the alpha-7 nicotinic receptor (α7nAChR). The association of CNV gains and losses with migraines will lead to better understanding of the molecular mechanisms and pathogenesis, to better define the disease, to be used as a treatment target.
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Affiliation(s)
- Mehmet Fatih Özaltun
- Department of Neurology, Gaziantep University, Gaziantep 27310, Turkey; (M.F.Ö.); (S.G.)
| | - Sırma Geyik
- Department of Neurology, Gaziantep University, Gaziantep 27310, Turkey; (M.F.Ö.); (S.G.)
| | - Şenay Görücü Yılmaz
- Department of Nutrition and Dietetics, Gaziantep University, Gaziantep 27310, Turkey
- Correspondence: or ; Tel.: +90-(342)-360-1200; Fax: +90-(342)-360-8795
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9
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Niestroj LM, Perez-Palma E, Howrigan DP, Zhou Y, Cheng F, Saarentaus E, Nürnberg P, Stevelink R, Daly MJ, Palotie A, Lal D. Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects. Brain 2020; 143:2106-2118. [PMID: 32568404 DOI: 10.1093/brain/awaa171] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 11/14/2022] Open
Abstract
Cytogenic testing is routinely applied in most neurological centres for severe paediatric epilepsies. However, which characteristics of copy number variants (CNVs) confer most epilepsy risk and which epilepsy subtypes carry the most CNV burden, have not been explored on a genome-wide scale. Here, we present the largest CNV investigation in epilepsy to date with 10 712 European epilepsy cases and 6746 ancestry-matched controls. Patients with genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, and developmental and epileptic encephalopathy were included. All samples were processed with the same technology and analysis pipeline. All investigated epilepsy types, including lesional focal epilepsy patients, showed an increase in CNV burden in at least one tested category compared to controls. However, we observed striking differences in CNV burden across epilepsy types and investigated CNV categories. Genetic generalized epilepsy patients have the highest CNV burden in all categories tested, followed by developmental and epileptic encephalopathy patients. Both epilepsy types also show association for deletions covering genes intolerant for truncating variants. Genome-wide CNV breakpoint association showed not only significant loci for genetic generalized and developmental and epileptic encephalopathy patients but also for lesional focal epilepsy patients. With a 34-fold risk for developing genetic generalized epilepsy, we show for the first time that the established epilepsy-associated 15q13.3 deletion represents the strongest risk CNV for genetic generalized epilepsy across the whole genome. Using the human interactome, we examined the largest connected component of the genes overlapped by CNVs in the four epilepsy types. We observed that genetic generalized epilepsy and non-acquired focal epilepsy formed disease modules. In summary, we show that in all common epilepsy types, 1.5-3% of patients carry epilepsy-associated CNVs. The characteristics of risk CNVs vary tremendously across and within epilepsy types. Thus, we advocate genome-wide genomic testing to identify all disease-associated types of CNVs.
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Affiliation(s)
- Lisa-Marie Niestroj
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany
| | - Eduardo Perez-Palma
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, FI-00014, Finland
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, 50931, Germany
| | - Remi Stevelink
- Department of Child Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, FI-00014, Finland.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aarno Palotie
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, FI-00014, Finland.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195 USA
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10
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Shademan B, Biray Avci C, Nikanfar M, Nourazarian A. Application of Next-Generation Sequencing in Neurodegenerative Diseases: Opportunities and Challenges. Neuromolecular Med 2020; 23:225-235. [PMID: 32399804 DOI: 10.1007/s12017-020-08601-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 12/28/2022]
Abstract
Genetic factors (gene mutations) lead to various rare and prevalent neurological diseases. Identification of underlying mutations in neurodegenerative diseases is of paramount importance due to the heterogeneous nature of the genome and different clinical manifestations. An early and accurate molecular diagnosis are cardinal for neurodegenerative patients to undergo proper therapeutic regimens. The next-generation sequencing (NGS) method examines up to millions of sequences at a time. As a result, the rare molecular diagnoses, previously presented with "unknown causes", are now possible in a short time. This method generates a large amount of data that can be utilized in patient management. Since each person has a unique genome, the NGS has transformed diagnostic and therapeutic strategies into sequencing and individual genomic mapping. However, this method has disadvantages like other diagnostic methods. Therefore, in this review, we aimed to briefly summarize the NGS method and correlated studies to unravel the genetic causes of neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, epilepsy, and MS. Finally, we discuss the NGS challenges and opportunities in neurodegenerative diseases.
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Affiliation(s)
- Behrouz Shademan
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey
| | - Cigir Biray Avci
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey.
| | - Masoud Nikanfar
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Nourazarian
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Golgasht St., 51666-16471, Tabriz, Iran. .,Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran.
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11
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Rosch R, Burrows DRW, Jones LB, Peters CH, Ruben P, Samarut É. Functional Genomics of Epilepsy and Associated Neurodevelopmental Disorders Using Simple Animal Models: From Genes, Molecules to Brain Networks. Front Cell Neurosci 2019; 13:556. [PMID: 31920556 PMCID: PMC6923670 DOI: 10.3389/fncel.2019.00556] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/02/2019] [Indexed: 01/06/2023] Open
Abstract
The genetic diagnosis of patients with seizure disorders has been improved significantly by the development of affordable next-generation sequencing technologies. Indeed, in the last 20 years, dozens of causative genes and thousands of associated variants have been described and, for many patients, are now considered responsible for their disease. However, the functional consequences of these mutations are often not studied in vivo, despite such studies being central to understanding pathogenic mechanisms and identifying novel therapeutic avenues. One main roadblock to functionally characterizing pathogenic mutations is generating and characterizing in vivo mammalian models carrying clinically relevant variants in specific genes identified in patients. Although the emergence of new mutagenesis techniques facilitates the production of rodent mutants, the fact that early development occurs internally hampers the investigation of gene function during neurodevelopment. In this context, functional genomics studies using simple animal models such as flies or fish are advantageous since they open a dynamic window of investigation throughout embryonic development. In this review, we will summarize how the use of simple animal models can fill the gap between genetic diagnosis and functional and phenotypic correlates of gene function in vivo. In particular, we will discuss how these simple animals offer the possibility to study gene function at multiple scales, from molecular function (i.e., ion channel activity), to cellular circuit and brain network dynamics. As a result, simple model systems offer alternative avenues of investigation to model aspects of the disease phenotype not currently possible in rodents, which can help to unravel the pathogenic substratum in vivo.
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Affiliation(s)
- Richard Rosch
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Paediatric Neurology, Great Ormond Street Hospital, NHS Foundation Trust, London, United Kingdom
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Dominic R. W. Burrows
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Laura B. Jones
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Colin H. Peters
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Peter Ruben
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Éric Samarut
- Department of Neurosciences, Research Center of the University of Montreal Hospital Center (CRCHUM), Université de Montréal, Montreal, QC, Canada
- Modelis Inc., Montreal, QC, Canada
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12
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Martín-Doncel E, Rojas AM, Cantarero L, Lazo PA. VRK1 functional insufficiency due to alterations in protein stability or kinase activity of human VRK1 pathogenic variants implicated in neuromotor syndromes. Sci Rep 2019; 9:13381. [PMID: 31527692 PMCID: PMC6746721 DOI: 10.1038/s41598-019-49821-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/30/2019] [Indexed: 12/12/2022] Open
Abstract
Very rare polymorphisms in the human VRK1 (vaccinia-related kinase 1) gene have been identified in complex neuromotor phenotypes associated to spinal muscular atrophy (SMA), pontocerebellar hypoplasia (PCH), microcephaly, amyotrophic lateral sclerosis (ALS) and distal motor neuron dysfunctions. The mechanisms by which these VRK1 variant proteins contribute to the pathogenesis of these neurological syndromes are unknown. The syndromes are manifested when both of these rare VRK1 polymorphic alleles are implicated, either in homozygosis or compound heterozygosis. In this report, to identify the common underlying pathogenic mechanism of VRK1 polymorphisms, we have studied all human VRK1 variants identified in these neurological phenotypes from a biochemical point of view by molecular modeling, protein stability and kinase activity assays. Molecular modelling predicted that VRK1 variant proteins are either unstable or have an altered kinase activity. The stability and kinase activity of VRK1 pathogenic variants detected two groups. One composed by variants with a reduced protein stability: R133C, R358X, L195V, G135R and R321C. The other group includes VRK1variants with a reduced kinase activity tested on several substrates: histones H3 and H2AX, p53, c-Jun, coilin and 53BP1, a DNA repair protein. VRK1 variants with reduced kinase activity are H119R, R133C, G135R, V236M, R321C and R358X. The common underlying effect of VRK1 pathogenic variants with reduced protein stability or kinase activity is a functional insufficiency of VRK1 in patients with neuromotor developmental syndromes. The G135 variant cause a defective formation of 53BP1 foci in response to DNA damage, and loss Cajal bodies assembled on coilin.
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Affiliation(s)
- Elena Martín-Doncel
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain
| | - Ana M Rojas
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Instituto de Biomedicina de Sevilla (IBIS), CSIC-Universidad de Sevilla, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Lara Cantarero
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain
- Laboratorio de Neurogenética y Medicina Molecular, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Pedro A Lazo
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Salamanca, Salamanca, Spain.
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain.
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13
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Papuc SM, Abela L, Steindl K, Begemann A, Simmons TL, Schmitt B, Zweier M, Oneda B, Socher E, Crowther LM, Wohlrab G, Gogoll L, Poms M, Seiler M, Papik M, Baldinger R, Baumer A, Asadollahi R, Kroell-Seger J, Schmid R, Iff T, Schmitt-Mechelke T, Otten K, Hackenberg A, Addor MC, Klein A, Azzarello-Burri S, Sticht H, Joset P, Plecko B, Rauch A. The role of recessive inheritance in early-onset epileptic encephalopathies: a combined whole-exome sequencing and copy number study. Eur J Hum Genet 2018; 27:408-421. [PMID: 30552426 PMCID: PMC6460568 DOI: 10.1038/s41431-018-0299-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 10/05/2018] [Accepted: 10/25/2018] [Indexed: 11/16/2022] Open
Abstract
Early-onset epileptic encephalopathy (EE) and combined developmental and epileptic encephalopathies (DEE) are clinically and genetically heterogeneous severely devastating conditions. Recent studies emphasized de novo variants as major underlying cause suggesting a generally low-recurrence risk. In order to better understand the full genetic landscape of EE and DEE, we performed high-resolution chromosomal microarray analysis in combination with whole-exome sequencing in 63 deeply phenotyped independent patients. After bioinformatic filtering for rare variants, diagnostic yield was improved for recessive disorders by manual data curation as well as molecular modeling of missense variants and untargeted plasma-metabolomics in selected patients. In total, we yielded a diagnosis in ∼42% of cases with causative copy number variants in 6 patients (∼10%) and causative sequence variants in 16 established disease genes in 20 patients (∼32%), including compound heterozygosity for causative sequence and copy number variants in one patient. In total, 38% of diagnosed cases were caused by recessive genes, of which two cases escaped automatic calling due to one allele occurring de novo. Notably, we found the recessive gene SPATA5 causative in as much as 3% of our cohort, indicating that it may have been underdiagnosed in previous studies. We further support candidacy for neurodevelopmental disorders of four previously described genes (PIK3AP1, GTF3C3, UFC1, and WRAP53), three of which also followed a recessive inheritance pattern. Our results therefore confirm the importance of de novo causative gene variants in EE/DEE, but additionally illustrate the major role of mostly compound heterozygous or hemizygous recessive inheritance and consequently high-recurrence risk.
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Affiliation(s)
- Sorina M Papuc
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland.,Victor Babes National Institute of Pathology, Bucharest, 050096, Romania
| | - Lucia Abela
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland.,CRC Clinical Research Center University, Children's Hospital Zurich, Zurich, 8032, Switzerland.,radiz-Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases University of Zurich, Zurich, 8032, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Thomas L Simmons
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Bernhard Schmitt
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland.,CRC Clinical Research Center University, Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Eileen Socher
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Lisa M Crowther
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Gabriele Wohlrab
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Laura Gogoll
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Martin Poms
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Michelle Seiler
- Pediatric Emergency Department, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Michael Papik
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Judith Kroell-Seger
- Children's department, Swiss Epilepsy Centre, Clinic Lengg, Zurich, 8000, Switzerland
| | - Regula Schmid
- Division of Child Neurology, Kantonsspital Winterthur, Winterthur, 8401, Switzerland
| | - Tobias Iff
- Municipal Hospital of Zurich Triemli, Zurich, 8063, Switzerland
| | | | - Karoline Otten
- Children's department, Swiss Epilepsy Centre, Clinic Lengg, Zurich, 8000, Switzerland
| | - Annette Hackenberg
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Marie-Claude Addor
- Department of Woman-Mother-Child, University Medical Center CHUV, Lausanne, 1015, Switzerland
| | - Andrea Klein
- Division of Paediatric Neurology, University Childerns Hospital Basel, UKBB, 4031, Basel, Switzerland.,Division of Paediatric Neurology, Development and Rehabilitation, University Children's Hospital, 3010, Bern, Switzerland
| | - Silvia Azzarello-Burri
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Barbara Plecko
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland.,CRC Clinical Research Center University, Children's Hospital Zurich, Zurich, 8032, Switzerland.,radiz-Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases University of Zurich, Zurich, 8032, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, 8057, Switzerland.,Division of General Pediatrics, Department of Pediatrics, Medical University of Graz, 8036, Graz, Austria
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland. .,radiz-Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases University of Zurich, Zurich, 8032, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, 8057, Switzerland. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, 8057, Switzerland.
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14
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Vijay A, Garg I, Ashraf MZ. Perspective: DNA Copy Number Variations in Cardiovascular Diseases. Epigenet Insights 2018; 11:2516865718818839. [PMID: 30560231 PMCID: PMC6291864 DOI: 10.1177/2516865718818839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022] Open
Abstract
Human genome contains many variations, often called mutations, which are difficult to detect and have remained a challenge for years. A substantial part of the genome encompasses repeats and when such repeats are in the coding region they may lead to change in the gene expression profile followed by pathological conditions. Structural variants are alterations which change one or more sequence feature in the chromosome such as change in the copy number, rearrangements, and translocations of a sequence and can be balanced or unbalanced. Copy number variants (CNVs) may increase or decrease the copies of a given region and have a pivotal role in the onset of many diseases including cardiovascular disorders. Cardiovascular disorders have a magnitude of well-established risk factors and etiology, but their correlation with CNVs is still being studied. In this article, we have discussed history of CNVs and a summary on the diseases associated with CNVs. To detect such variations, we shed light on the number of techniques introduced so far and their limitations. The lack of studies on cardiovascular diseases to determine the frequency of such variants needs clinical studies with larger cohorts. This review is a compilation of articles suggesting the importance of CNVs in multitude of cardiovascular anomalies. Finally, future perspectives for better understanding of CNVs and cardiovascular disorders have also been discussed.
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Affiliation(s)
- Aatira Vijay
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Iti Garg
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Mohammad Zahid Ashraf
- Genomics Division, Defence Institute of Physiology and Allied Sciences, DRDO, Delhi, India
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15
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Jabbari K, Bobbili DR, Lal D, Reinthaler EM, Schubert J, Wolking S, Sinha V, Motameny S, Thiele H, Kawalia A, Altmüller J, Toliat MR, Kraaij R, van Rooij J, Uitterlinden AG, Ikram MA, Zara F, Lehesjoki AE, Krause R, Zimprich F, Sander T, Neubauer BA, May P, Lerche H, Nürnberg P. Rare gene deletions in genetic generalized and Rolandic epilepsies. PLoS One 2018; 13:e0202022. [PMID: 30148849 PMCID: PMC6110470 DOI: 10.1371/journal.pone.0202022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/26/2018] [Indexed: 12/30/2022] Open
Abstract
Genetic Generalized Epilepsy (GGE) and benign epilepsy with centro-temporal spikes or Rolandic Epilepsy (RE) are common forms of genetic epilepsies. Rare copy number variants have been recognized as important risk factors in brain disorders. We performed a systematic survey of rare deletions affecting protein-coding genes derived from exome data of patients with common forms of genetic epilepsies. We analysed exomes from 390 European patients (196 GGE and 194 RE) and 572 population controls to identify low-frequency genic deletions. We found that 75 (32 GGE and 43 RE) patients out of 390, i.e. ~19%, carried rare genic deletions. In particular, large deletions (>400 kb) represent a higher burden in both GGE and RE syndromes as compared to controls. The detected low-frequency deletions (1) share genes with brain-expressed exons that are under negative selection, (2) overlap with known autism and epilepsy-associated candidate genes, (3) are enriched for CNV intolerant genes recorded by the Exome Aggregation Consortium (ExAC) and (4) coincide with likely disruptive de novo mutations from the NPdenovo database. Employing several knowledge databases, we discuss the most prominent epilepsy candidate genes and their protein-protein networks for GGE and RE.
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Affiliation(s)
- Kamel Jabbari
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Cologne Biocenter, Institute for Genetics, University of Cologne, Cologne, Germany
| | - Dheeraj R. Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Eva M. Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Julian Schubert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Stefan Wolking
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Vishal Sinha
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Susanne Motameny
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Amit Kawalia
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | | | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - M. Arfan Ikram
- Departments of Epidemiology, Neurology, and Radiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, Institute G. Gaslini, Genova, Italy
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Neuroscience Center and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, Medical Faculty University Giessen, Giessen, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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16
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Addis L, Sproviero W, Thomas SV, Caraballo RH, Newhouse SJ, Gomez K, Hughes E, Kinali M, McCormick D, Hannan S, Cossu S, Taylor J, Akman CI, Wolf SM, Mandelbaum DE, Gupta R, van der Spek RA, Pruna D, Pal DK. Identification of new risk factors for rolandic epilepsy: CNV at Xp22.31 and alterations at cholinergic synapses. J Med Genet 2018; 55:607-616. [PMID: 29789371 PMCID: PMC6119347 DOI: 10.1136/jmedgenet-2018-105319] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/18/2018] [Accepted: 04/28/2018] [Indexed: 12/25/2022]
Abstract
Background Rolandic epilepsy (RE) is the most common genetic childhood epilepsy, consisting of focal, nocturnal seizures and frequent neurodevelopmental impairments in speech, language, literacy and attention. A complex genetic aetiology is presumed in most, with monogenic mutations in GRIN2A accounting for >5% of cases. Objective To identify rare, causal CNV in patients with RE. Methods We used high-density SNP arrays to analyse the presence of rare CNVs in 186 patients with RE from the UK, the USA, Sardinia, Argentina and Kerala, India. Results We identified 84 patients with one or more rare CNVs, and, within this group, 14 (7.5%) with recurrent risk factor CNVs and 15 (8.0%) with likely pathogenic CNVs. Nine patients carried recurrent hotspot CNVs including at 16p13.11 and 1p36, with the most striking finding that four individuals (three from Sardinia) carried a duplication, and one a deletion, at Xp22.31. Five patients with RE carried a rare CNV that disrupted genes associated with other epilepsies (KCTD7, ARHGEF15, CACNA2D1, GRIN2A and ARHGEF4), and 17 cases carried CNVs that disrupted genes associated with other neurological conditions or that are involved in neuronal signalling/development. Network analysis of disrupted genes with high brain expression identified significant enrichment in pathways of the cholinergic synapse, guanine-exchange factor activation and the mammalian target of rapamycin. Conclusion Our results provide a CNV profile of an ethnically diverse cohort of patients with RE, uncovering new areas of research focus, and emphasise the importance of studying non-western European populations in oligogenic disorders to uncover a full picture of risk variation.
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Affiliation(s)
- Laura Addis
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,Neuroscience Discovery Research, Eli Lilly and Company, Surrey, UK
| | - William Sproviero
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Sanjeev V Thomas
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, Kerala, India
| | - Roberto H Caraballo
- Department of Neurology, Hospital de Pediatría Prof. Dr. J.P. Garrahan, Combate de los Pozos 1881, Buenos Aires, Argentina
| | - Stephen J Newhouse
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Beckenham, UK.,Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
| | - Kumudini Gomez
- Department of Paediatrics, University Hospital Lewisham, Lewisham and Greenwich NHS Trust, London, UK
| | - Elaine Hughes
- Department of Paediatric Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, London, UK
| | - Maria Kinali
- Department of Paediatric Neurology, Chelsea and Westminster Hospital, London, UK
| | - David McCormick
- Department of Paediatric Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, London, UK
| | - Siobhan Hannan
- Department of Paediatric Neurology, Chelsea and Westminster Hospital, London, UK
| | - Silvia Cossu
- Neurosurgery Unit, Neuroscience and Neurorehabilitation Department, Bambino Gesù Children Hospital, Rome, Italy.,Neurology Unit, Pediatric Hospital A. Cao, Brotzu Hospital Trust, Cagliari, Italy
| | | | - Cigdem I Akman
- Division of Pediatric Neurology, College of Physicians and Surgeons of Columbia University, New York City, New York, USA
| | - Steven M Wolf
- Department of Neurology, Mount Sinai Health System, New York City, New York, USA
| | - David E Mandelbaum
- Departments of Pediatrics, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Rajesh Gupta
- Department of Paediatrics, Tunbridge Wells Hospital, Pembury, UK
| | - Rick A van der Spek
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dario Pruna
- Neurology Unit, Pediatric Hospital A. Cao, Brotzu Hospital Trust, Cagliari, Italy
| | - Deb K Pal
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
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17
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Monlong J, Girard SL, Meloche C, Cadieux-Dion M, Andrade DM, Lafreniere RG, Gravel M, Spiegelman D, Dionne-Laporte A, Boelman C, Hamdan FF, Michaud JL, Rouleau G, Minassian BA, Bourque G, Cossette P. Global characterization of copy number variants in epilepsy patients from whole genome sequencing. PLoS Genet 2018; 14:e1007285. [PMID: 29649218 PMCID: PMC5978987 DOI: 10.1371/journal.pgen.1007285] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/24/2018] [Accepted: 03/04/2018] [Indexed: 12/17/2022] Open
Abstract
Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs. Using WGS and PopSV, we performed a comprehensive characterization of CNVs in 198 individuals affected with epilepsy and 301 controls. For both large and small variants, we found an enrichment of rare exonic events in epilepsy patients, especially in genes with predicted loss-of-function intolerance. Notably, this genome-wide survey also revealed an enrichment of rare non-coding CNVs near previously known epilepsy genes. This enrichment was strongest for non-coding CNVs located within 100 Kbp of an epilepsy gene and in regions associated with changes in the gene expression, such as expression QTLs or DNase I hypersensitive sites. Finally, we report on 21 potentially damaging events that could be associated with known or new candidate epilepsy genes. Our results suggest that comprehensive sequence-based profiling of CNVs could help explain a larger fraction of epilepsy cases.
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Affiliation(s)
- Jean Monlong
- Department of Human Genetics, McGill University, Montréal, Canada
- Canadian Center for Computational Genomics, Montréal, Canada
| | - Simon L. Girard
- Department of Human Genetics, McGill University, Montréal, Canada
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Caroline Meloche
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Maxime Cadieux-Dion
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
- Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, Missouri, United States of America
| | - Danielle M. Andrade
- Epilepsy Genetics Program, Division of Neurology, Toronto Western Hospital, University of Toronto, Toronto, Canada
| | - Ron G. Lafreniere
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Micheline Gravel
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montréal, Canada
| | | | - Cyrus Boelman
- Division of Neurology, BC Children’s Hospital, Vancouver, Canada
| | | | | | - Guy Rouleau
- Montreal Neurological Institute, McGill University, Montréal, Canada
| | | | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Canada
- Canadian Center for Computational Genomics, Montréal, Canada
- McGill University and Génome Québec Innovation Center, Montréal, Canada
- * E-mail: (GB); (PC)
| | - Patrick Cossette
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
- * E-mail: (GB); (PC)
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Dunn P, Albury CL, Maksemous N, Benton MC, Sutherland HG, Smith RA, Haupt LM, Griffiths LR. Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes. Front Genet 2018; 9:20. [PMID: 29467791 PMCID: PMC5808353 DOI: 10.3389/fgene.2018.00020] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/16/2018] [Indexed: 12/28/2022] Open
Abstract
Epilepsy is a neurological disorder characterized by an increased predisposition for seizures. Although this definition suggests that it is a single disorder, epilepsy encompasses a group of disorders with diverse aetiologies and outcomes. A genetic basis for epilepsy syndromes has been postulated for several decades, with several mutations in specific genes identified that have increased our understanding of the genetic influence on epilepsies. With 70-80% of epilepsy cases identified to have a genetic cause, there are now hundreds of genes identified to be associated with epilepsy syndromes which can be analyzed using next generation sequencing (NGS) techniques such as targeted gene panels, whole exome sequencing (WES) and whole genome sequencing (WGS). For effective use of these methodologies, diagnostic laboratories and clinicians require information on the relevant workflows including analysis and sequencing depth to understand the specific clinical application and diagnostic capabilities of these gene sequencing techniques. As epilepsy is a complex disorder, the differences associated with each technique influence the ability to form a diagnosis along with an accurate detection of the genetic etiology of the disorder. In addition, for diagnostic testing, an important parameter is the cost-effectiveness and the specific diagnostic outcome of each technique. Here, we review these commonly used NGS techniques to determine their suitability for application to epilepsy genetic diagnostic testing.
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Affiliation(s)
- Paul Dunn
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Cassie L Albury
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Neven Maksemous
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Miles C Benton
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Heidi G Sutherland
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Robert A Smith
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Larisa M Haupt
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
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20
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Knox AT, Glauser T, Tenney J, Lytton WW, Holland K. Modeling pathogenesis and treatment response in childhood absence epilepsy. Epilepsia 2017; 59:135-145. [PMID: 29265352 DOI: 10.1111/epi.13962] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Childhood absence epilepsy (CAE) is a genetic generalized epilepsy syndrome with polygenic inheritance, with genes for γ-aminobutyric acid (GABA) receptors and T-type calcium channels implicated in the disorder. Previous studies of T-type calcium channel electrophysiology have shown genetic changes and medications have multiple effects. The aim of this study was to use an established thalamocortical computer model to determine how T-type calcium channels work in concert with cortical excitability to contribute to pathogenesis and treatment response in CAE. METHODS The model is comprised of cortical pyramidal, cortical inhibitory, thalamocortical relay, and thalamic reticular single-compartment neurons, implemented with Hodgkin-Huxley model ion channels and connected by AMPA, GABAA , and GABAB synapses. Network behavior was simulated for different combinations of T-type calcium channel conductance, inactivation time, steady state activation/inactivation shift, and cortical GABAA conductance. RESULTS Decreasing cortical GABAA conductance and increasing T-type calcium channel conductance converted spindle to spike and wave oscillations; smaller changes were required if both were changed in concert. In contrast, left shift of steady state voltage activation/inactivation did not lead to spike and wave oscillations, whereas right shift reduced network propensity for oscillations of any type. SIGNIFICANCE These results provide a window into mechanisms underlying polygenic inheritance in CAE, as well as a mechanism for treatment effects and failures mediated by these channels. Although the model is a simplification of the human thalamocortical network, it serves as a useful starting point for predicting the implications of ion channel electrophysiology in polygenic epilepsy such as CAE.
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Affiliation(s)
- Andrew T Knox
- Department of Neurology, University of Wisconsin, Madison, WI, USA
| | - Tracy Glauser
- Comprehensive Epilepsy Center, Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,The University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jeffrey Tenney
- Comprehensive Epilepsy Center, Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,The University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William W Lytton
- Departments of Neurology and Physiology & Pharmacology, SUNY Downstate Medical Center, Brooklyn, NY, USA.,Department Neurology, Kings County Hospital Center, Brooklyn, NY, USA
| | - Katherine Holland
- Comprehensive Epilepsy Center, Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,The University of Cincinnati College of Medicine, Cincinnati, OH, USA
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Borlot F, Regan BM, Bassett AS, Stavropoulos DJ, Andrade DM. Prevalence of Pathogenic Copy Number Variation in Adults With Pediatric-Onset Epilepsy and Intellectual Disability. JAMA Neurol 2017; 74:1301-1311. [PMID: 28846756 DOI: 10.1001/jamaneurol.2017.1775] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Importance Copy number variation (CNV) is an important cause of neuropsychiatric disorders. Little is known about the role of CNV in adults with epilepsy and intellectual disability. Objectives To evaluate the prevalence of pathogenic CNVs and identify possible candidate CNVs and genes in patients with epilepsy and intellectual disability. Design, Setting, and Participants In this cross-sectional study, genome-wide microarray was used to evaluate a cohort of 143 adults with unexplained childhood-onset epilepsy and intellectual disability who were recruited from the Toronto Western Hospital epilepsy outpatient clinic from January 1, 2012, through December 31, 2014. The inclusion criteria were (1) pediatric seizure onset with ongoing seizure activity in adulthood, (2) intellectual disability of any degree, and (3) no structural brain abnormalities or metabolic conditions that could explain the seizures. Main Outcomes and Measures DNA screening was performed using genome-wide microarray platforms. Pathogenicity of CNVs was assessed based on the American College of Medical Genetics guidelines. The Residual Variation Intolerance Score was used to evaluate genes within the identified CNVs that could play a role in each patient's phenotype. Results Of the 2335 patients, 143 probands were investigated (mean [SD] age, 24.6 [10.8] years; 69 male and 74 female). Twenty-three probands (16.1%) and 4 affected relatives (2.8%) (mean [SD] age, 24.1 [6.1] years; 11 male and 16 female) presented with pathogenic or likely pathogenic CNVs (0.08-18.9 Mb). Five of the 23 probands with positive results (21.7%) had more than 1 CNV reported. Parental testing revealed de novo CNVs in 11 (47.8%), with CNVs inherited from a parent in 4 probands (17.4%). Sixteen of 23 probands (69.6%) presented with previously cataloged human genetic disorders and/or defined CNV hot spots in epilepsy. Eight nonrecurrent rare CNVs that overlapped 1 or more genes associated with intellectual disability, autism, and/or epilepsy were identified: 2p16.1-p15 duplication, 6p25.3-p25.1 duplication, 8p23.3p23.1 deletion, 9p24.3-p23 deletion, 10q11.22-q11.23 duplication, 12p13.33-13.2 duplication, 13q34 deletion, and 16p13.2 duplication. Five genes are of particular interest given their potential pathogenicity in the corresponding phenotypes and least tolerability to variation: ABAT, KIAA2022, COL4A1, CACNA1C, and SMARCA2. ABAT duplication was associated with Lennox-Gastaut syndrome and KIAA2022 deletion with Jeavons syndrome. Conclusions and Relevance The high prevalence of pathogenic CNVs in this study highlights the importance of microarray analysis in adults with unexplained childhood-onset epilepsy and intellectual disability. Additional studies and comparison with similar cases are required to evaluate the effects of deletions and duplications that overlap specific genes.
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Affiliation(s)
- Felippe Borlot
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada.,Clinical Neurosciences Center, Department of Neurology, University of Utah, Salt Lake City
| | - Brigid M Regan
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - D James Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Danielle M Andrade
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada.,Division of Neurology, Krembil Neuroscience Centre, Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada
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Marquet V, Bourthoumieu S, Dobrescu A, Laroche-Raynaud C, Yardin C. Familial 1p36.3 microduplication resulting from a 1p-9q non-reciprocal translocation. Eur J Med Genet 2017; 60:583-588. [PMID: 28811188 DOI: 10.1016/j.ejmg.2017.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/22/2017] [Accepted: 08/10/2017] [Indexed: 10/19/2022]
Abstract
Unlike the 1p36 microdeletion syndrome, which has been extensively described, 1p36 microduplications have rarely been reported. We describe a three years old boy presenting with a severe global developmental delay and a few dysmorphic features. Cytogenetic analyses revealed a maternally inherited 3.35 Mb microduplication of chromosomal band 1p36.3. The maternal grandfather is also carrier of the same chromosomal rearrangement. Interestingly, the duplicated 1p36.3 segment was found to be localized at the telomeric end of the long arms of a chromosome 9, probably deriving from a 1p36.3-9qter non-reciprocal translocation. This particular type of chromosomal translocation has rarely been reported, and its mechanism is unclear. The phenotypical features associated with 1p36.3 microduplication vary due to the non-recurrent breakpoints of the rearrangements in this particular region. However when compiling the few described cases the phenotypical spectrum seems to include mainly developmental delay, mild facial dysmorphism, and neurological, cardiac and skeletal anomalies. The description of new patients carrying a 1p36.3 duplication like ours will lead to further delineation of the phenotypical spectrum and may help to find critical regions and causative genes implicated in the phenotype.
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Affiliation(s)
- Valentine Marquet
- Department of Cytology, Histology, Cytogenetics and Cellular Biology, Limoges University Hospital, France.
| | - Sylvie Bourthoumieu
- Department of Cytology, Histology, Cytogenetics and Cellular Biology, Limoges University Hospital, France
| | - Amelia Dobrescu
- Department of Cytology, Histology, Cytogenetics and Cellular Biology, Limoges University Hospital, France
| | | | - Catherine Yardin
- Department of Cytology, Histology, Cytogenetics and Cellular Biology, Limoges University Hospital, France; Limoges University, CNRS, XLIM, UMR 7252, F-87000 Limoges, France
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Rezazadeh A, Borlot F, Faghfoury H, Andrade DM. Genetic generalized epilepsy in three siblings with 8q21.13-q22.2 duplication. Seizure 2017; 48:57-61. [DOI: 10.1016/j.seizure.2017.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 04/05/2017] [Indexed: 12/24/2022] Open
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Klein CJ, Foroud TM. Neurology Individualized Medicine: When to Use Next-Generation Sequencing Panels. Mayo Clin Proc 2017; 92:292-305. [PMID: 28160876 DOI: 10.1016/j.mayocp.2016.09.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/17/2016] [Accepted: 09/09/2016] [Indexed: 01/05/2023]
Abstract
Next-generation sequencing (NGS) is increasingly being applied to clinical testing. This practice is predicted to grow especially in neurology clinics because many of their patients have monogenetic causes for their "diagnostic odyssey." The cost of sequencing has been steadily decreasing, but the cost of DNA sequencing is a minor part of the total cost. Downstream data analysis, storage, and interpretation account for most of the total expense. In patients with nonspecific neurologic disorders in which an extensive number of genetic differential diagnoses exist, whole-genome sequencing (WGS) or whole-exome sequencing (WES) has shown promise in the identification of genetic causes. However, both WGS and WES have incomplete coverage and produce a large number of rare variants of unknown importance. In addition, ethical dilemmas are often created by unexpected findings in genes unrelated to the initial sequencing indication. Targeted-panel NGS starts with the capture of a set of disease-focused genes, followed by massive parallel sequencing. For many genetically heterogeneous neurologic disorders, a genetic panel that is disease focused yet inclusive of a large genetic differential diagnosis can be defined to reduce cost, increase turnaround time, and optimize performance. Targeted-panel NGS is currently the preferred first-tier approach because it provides a reliable clinical application while eliminating unexpected ethical dilemmas. Targeted-panel NGS is leading to a paradigm shift in the diagnosis of many neurologic disorders, enabling individualized precision medicine. In this review, we provide an overview of WGS, WES, and targeted-panel NGS in consideration of their utility in clinical testing for neurologic diseases.
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Affiliation(s)
- Christopher J Klein
- Department of Neurology and Department of Medical Genetics, Mayo Clinic, Rochester, MN.
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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Affiliation(s)
- Chantal Depondt
- Department of Neurology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
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