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Fasaludeen A, McTague A, Jose M, Banerjee M, Sundaram S, Madhusoodanan UK, Radhakrishnan A, Menon RN. Genetic variant interpretation for the neurologist - A pragmatic approach in the next-generation sequencing era in childhood epilepsy. Epilepsy Res 2024; 201:107341. [PMID: 38447235 DOI: 10.1016/j.eplepsyres.2024.107341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Genetic advances over the past decade have enhanced our understanding of the genetic landscape of childhood epilepsy. However a major challenge for clinicians ha been understanding the rationale and systematic approach towards interpretation of the clinical significance of variant(s) detected in their patients. As the clinical paradigm evolves from gene panels to whole exome or whole genome testing including rapid genome sequencing, the number of patients tested and variants identified per patient will only increase. Each step in the process of variant interpretation has limitations and there is no single criterion which enables the clinician to draw reliable conclusions on a causal relationship between the variant and disease without robust clinical phenotyping. Although many automated online analysis software tools are available, these carry a risk of misinterpretation. This guideline provides a pragmatic, real-world approach to variant interpretation for the child neurologist. The focus will be on ascertaining aspects such as variant frequency, subtype, inheritance pattern, structural and functional consequence with regard to genotype-phenotype correlations, while refraining from mere interpretation of the classification provided in a genetic test report. It will not replace the expert advice of colleagues in clinical genetics, however as genomic investigations become a first-line test for epilepsy, it is vital that neurologists and epileptologists are equipped to navigate this landscape.
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Affiliation(s)
- Alfiya Fasaludeen
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Amy McTague
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
| | - Manna Jose
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Soumya Sundaram
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - U K Madhusoodanan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ashalatha Radhakrishnan
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ramshekhar N Menon
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India.
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2
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
| | - Caroline F. Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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3
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Dahawi M, Elmagzoub MS, A. Ahmed E, Baldassari S, Achaz G, Elmugadam FA, Abdelgadir WA, Baulac S, Buratti J, Abdalla O, Gamil S, Alzubeir M, Abubaker R, Noé E, Elsayed L, Ahmed AE, Leguern E. Involvement of ADGRV1 Gene in Familial Forms of Genetic Generalized Epilepsy. Front Neurol 2021; 12:738272. [PMID: 34744978 PMCID: PMC8567843 DOI: 10.3389/fneur.2021.738272] [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: 07/08/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022] Open
Abstract
Background: Genetic generalized epilepsies (GGE) including childhood absence epilepsy (CAE), juvenile absence epilepsy (JAE), juvenile myoclonic epilepsy (JME), and GGE with tonic-clonic seizures alone (GGE-TCS), are common types of epilepsy mostly determined by a polygenic mode of inheritance. Recent studies showed that susceptibility genes for GGE are numerous, and their variants rare, challenging their identification. In this study, we aimed to assess GGE genetic etiology in a Sudanese population. Methods: We performed whole-exome sequencing (WES) on DNA of 40 patients from 20 Sudanese families with GGE searching for candidate susceptibility variants, which were prioritized by CADD software and functional features of the corresponding gene. We assessed their segregation in 138 individuals and performed genotype-phenotype correlations. Results: In a family including three sibs with GGE-TCS, we identified a rare missense variant in ADGRV1 encoding an adhesion G protein-coupled receptor V1, which was already involved in the autosomal recessive Usher type C syndrome. In addition, five other ADGRV1 rare missense variants were identified in four additional families and absent from 119 Sudanese controls. In one of these families, an ADGRV1 variant was found at a homozygous state, in a female more severely affected than her heterozygous brother, suggesting a gene dosage effect. In the five families, GGE phenotype was statistically associated with ADGRV1 variants (0R = 0.9 103). Conclusion: This study highly supports, for the first time, the involvement of ADGRV1 missense variants in familial GGE and that ADGRV1 is a susceptibility gene for CAE/JAE and GGE-TCS phenotypes.
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Affiliation(s)
- Maha Dahawi
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Department of Physiology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mohamed S. Elmagzoub
- Faculty of Medicine, National Ribat University, Khartoum, Sudan
- Neuroscience Department, College of Applied Medical Sciences, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Elhami A. Ahmed
- UNESCO Chair on Bioethics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sara Baldassari
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- SMILE Group, CIRB, Collège de France, CNRS, INSERM, Paris, France
- Éco-anthropologie, Muséum National d'Histoire Naturelle, Université de Paris, Paris, France
| | | | - Wasma A. Abdelgadir
- Department of Biochemistry and Molecular Biology, Faculty of Sciences and Technology, Al-Neelain University, Khartoum, Sudan
| | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Julien Buratti
- Department of Medical Genetics, AP-HP Sorbonne Université, Sorbonne Université, Paris, France
| | - Omer Abdalla
- Department of Physiology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sahar Gamil
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha Alzubeir
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Neurology, Sudan Medical Council, Khartoum, Sudan
| | - Rayan Abubaker
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Eric Noé
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Sorbonne Université, Paris, France
| | - Liena Elsayed
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Department of Basic Sciences, College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ammar E. Ahmed
- Department of Physiology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Neurology, Sudan Medical Council, Khartoum, Sudan
| | - Eric Leguern
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Department of Medical Genetics, AP-HP Sorbonne Université, Sorbonne Université, Paris, France
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4
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Mutational Analysis of Myoclonin1 Gene in Pakistani Juvenile Myoclonic Epilepsy Patients. BIOMED RESEARCH INTERNATIONAL 2021; 2021:7509825. [PMID: 33969125 PMCID: PMC8081613 DOI: 10.1155/2021/7509825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 02/03/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023]
Abstract
Juvenile myoclonic epilepsy (JME) is the most prevalent and genetically heterogeneous form of epilepsy and accounts for 10–30% of all the cases worldwide. Ef-hand domain- (c-terminal-) containing protein 1 (EFHC1) encodes for a nonion channel protein and mutations in this gene have been extensively reported in different populations to play a causative role in JME. Linkage between JME and 6p11-12 locus has already been confirmed in Mexican and Dutch families. A case-control study was conducted on Pakistani JME patients for the first time, aimed at finding out EFHC1 mutations that have been reported in different populations. For this purpose, 66 clinically diagnosed JME patients and 108 control subjects were included in the study. Blood samples were collected from all the participants, and DNA was isolated from the lymphocytes by the modified organic method. Total 3 exons of EFHC1, harboring extensively reported mutations, were selected for genotypic analysis. We identified three heterozygous variants, R159W, V460A, P436P, and one insertion in the current study. V460A, an uncommon variant identified herein, has recently been reported in public databases in an unphenotyped American individual. This missense variant was found in 3 Pakistani JME patients from 2 unrelated families. However, in silico analysis showed that V460A may possibly be a neutral variant. While the absence of a majority of previously reported mutations in our population suggests that most of the mutations of EFHC1 are confined to particular ethnicities and are not evenly distributed across the world. However, to imply the causation, the whole gene and larger number of JME patients should be screened in this understudied population.
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5
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Gonsales MC, Ribeiro PAO, Betting LE, Alvim MKM, Guerreiro CM, Yasuda CL, Gitaí DLG, Cendes F, Lopes-Cendes I. Revisiting the clinical impact of variants in EFHC1 in patients with different phenotypes of genetic generalized epilepsy. Epilepsy Behav 2020; 112:107469. [PMID: 33181902 DOI: 10.1016/j.yebeh.2020.107469] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/20/2020] [Accepted: 08/30/2020] [Indexed: 01/27/2023]
Abstract
The most common form of genetic generalized epilepsy (GGE) is juvenile myoclonic epilepsy (JME), which accounts for 5 to 10% of all epilepsy cases. The gene EFHC1 has been implicated as a putative cause of JME. However, it remains debatable whether testing for EFHC1 mutations should be included in the diagnostic epilepsy gene panels. To investigate the clinical utility of EFHC1 testing, we studied 125 individuals: 100 with JME and 25 with other GGEs. We amplified and sequenced all EFHC1 coding exons. Then, we predicted the pathogenicity or benign impact of the variants using the analyses proposed by the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP). Mutation screening revealed 11 missense variants in 44 probands with JME (44%) and one of the seven individuals with generalized tonic-clonic seizures on awakening (14%). Six of the 11 variants (54%) were classified as 'benign,' and the remaining variants were considered variants of uncertain significance (VUS). There is currently a limitation to test for genes that predispose an individual to complex, nonmonogenic phenotypes. Thus, we show suggestive evidence that EFHC1 testing lacks a scientific foundation based on the disputed nature of the gene-disease relationship and should be currently limited to research purposes.
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Affiliation(s)
- Marina C Gonsales
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil; The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Patrícia A O Ribeiro
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil; The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Luiz E Betting
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil; The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Marina K M Alvim
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil; The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Carlos M Guerreiro
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil; The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Clarissa L Yasuda
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil; The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Daniel L G Gitaí
- Institute of Biological Sciences and Health, Federal University of Alagoas (UFAL), Maceió, AL, Brazil
| | - Fernando Cendes
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil; The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil; The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.
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6
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Ma M, Stoyanova M, Rademacher G, Dutcher SK, Brown A, Zhang R. Structure of the Decorated Ciliary Doublet Microtubule. Cell 2019; 179:909-922.e12. [PMID: 31668805 PMCID: PMC6936269 DOI: 10.1016/j.cell.2019.09.030] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/29/2019] [Accepted: 09/23/2019] [Indexed: 02/02/2023]
Abstract
The axoneme of motile cilia is the largest macromolecular machine of eukaryotic cells. In humans, impaired axoneme function causes a range of ciliopathies. Axoneme assembly, structure, and motility require a radially arranged set of doublet microtubules, each decorated in repeating patterns with non-tubulin components. We use single-particle cryo-electron microscopy to visualize and build an atomic model of the repeating structure of a native axonemal doublet microtubule, which reveals the identities, positions, repeat lengths, and interactions of 38 associated proteins, including 33 microtubule inner proteins (MIPs). The structure demonstrates how these proteins establish the unique architecture of doublet microtubules, maintain coherent periodicities along the axoneme, and stabilize the microtubules against the repeated mechanical stress induced by ciliary motility. Our work elucidates the architectural principles that underpin the assembly of this large, repetitive eukaryotic structure and provides a molecular basis for understanding the etiology of human ciliopathies.
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Affiliation(s)
- Meisheng Ma
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Mihaela Stoyanova
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Griffin Rademacher
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.
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7
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Ellis CA, Petrovski S, Berkovic SF. Epilepsy genetics: clinical impacts and biological insights. Lancet Neurol 2019; 19:93-100. [PMID: 31494011 DOI: 10.1016/s1474-4422(19)30269-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 05/18/2019] [Accepted: 06/11/2019] [Indexed: 01/23/2023]
Abstract
Genomics now has an increasingly important role in neurology clinics. Regarding the epilepsies, innovations centred around technology, analytics, and collaboration have led to remarkable progress in gene discovery and have revealed the diverse array of genetic mechanisms and neurobiological pathways that contribute to these disorders. The new genomic era can present a challenge to clinicians, who now find themselves asked to interpret and apply genetic data to their daily management of patients with epilepsy. Navigation of this new era will require genetic literacy and familiarity with research advances in epilepsy genetics. Genetic epilepsy diagnoses now directly affect clinical care, and their importance will only increase as new targeted treatments continue to emerge. At the same time, new genetic insights challenge us to move from a deterministic view of genetic changes to a more nuanced appreciation of genetic risk within complex neurobiological systems that give rise to epilepsy.
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Affiliation(s)
- Colin A Ellis
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA; Epilepsy Research Centre, Department of Medicine, University of Melbourne (Austin Health), Heidelberg, VIC, Australia
| | - Slavé Petrovski
- Epilepsy Research Centre, Department of Medicine, University of Melbourne (Austin Health), Heidelberg, VIC, Australia; Centre for Genomics Research, Discovery Sciences, Research and Development Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne (Austin Health), Heidelberg, VIC, Australia.
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8
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Clinical and genetic study of Tunisian families with genetic generalized epilepsy: contribution of CACNA1H and MAST4 genes. Neurogenetics 2018; 19:165-178. [PMID: 29948376 DOI: 10.1007/s10048-018-0550-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/11/2022]
Abstract
Genetic generalized epilepsies (GGE) (childhood absence epilepsy (CAE), juvenile myoclonic epilepsy (JME) and epilepsy with generalized tonic-clonic seizures (GTCS)) are mainly determined by genetic factors. Since few mutations were identified in rare families with autosomal dominant GGE, a polygenic inheritance was suspected in most patients. Recent studies on large American or European cohorts of sporadic cases showed that susceptibility genes were numerous although their variants were rare, making their identification difficult. Here, we reported clinical and genetic characteristics of 30 Tunisian GGE families, including 71 GGE patients. The phenotype was close to that in sporadic cases. Nineteen pedigrees had a homogeneous type of GGE (JME-CAE-CGTS), and 11 combined these epileptic syndromes. Rare non-synonymous variants were selected in probands using a targeted panel of 30 candidate genes and their segregation was determined in families. Molecular studies incriminated different genes, mainly CACNA1H and MAST4. The segregation of at least two variants in different genes in some pedigrees was compatible with the hypothesis of an oligogenic inheritance, which was in accordance with the relatively low frequency of consanguineous probands. Since at least 2 susceptibility genes were likely shared by different populations, genetic factors involved in the majority of Tunisian GGE families remain to be discovered. Their identification should be easier in families with a homogeneous type of GGE, in which an intra-familial genetic homogeneity could be suspected.
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9
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Helbig I, Heinzen EL, Mefford HC. Genetic literacy series: Primer part 2-Paradigm shifts in epilepsy genetics. Epilepsia 2018; 59:1138-1147. [PMID: 29741288 DOI: 10.1111/epi.14193] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2018] [Indexed: 01/05/2023]
Abstract
This is the second of a 2-part primer on the genetics of the epilepsies within the Genetic Literacy Series of the Genetics Commission of the International League Against Epilepsy. In Part 1, we covered types of genetic variation, inheritance patterns, and their relationship to disease. In Part 2, we apply these basic principles to the case of a young boy with epileptic encephalopathy and ask 3 important questions: (1) Is the gene in question an established genetic etiology for epilepsy? (2) Is the variant in this particular gene pathogenic by established variant interpretation criteria? (3) Is the variant considered causative in the clinical context? These questions are considered and then answered for the clinical case in question.
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Affiliation(s)
- Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
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10
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Helbig I. Commentary: The genetic architecture of the epilepsies, as told by 8500 gene panels. Epilepsia 2018; 59:1072-1073. [DOI: 10.1111/epi.14075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ingo Helbig
- Division of Neurology The Children's Hospital of Philadelphia Philadelphia PA USA
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11
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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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12
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Steward CA, Parker APJ, Minassian BA, Sisodiya SM, Frankish A, Harrow J. Genome annotation for clinical genomic diagnostics: strengths and weaknesses. Genome Med 2017; 9:49. [PMID: 28558813 PMCID: PMC5448149 DOI: 10.1186/s13073-017-0441-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number of patients, the genetic basis remains unclear. As clinicians begin to consider whole-genome sequencing, an understanding of the processes and tools involved and the factors to consider in the annotation of the structure and function of genomic elements that might influence variant identification is crucial. Here, we discuss and illustrate the strengths and weaknesses of approaches for the annotation and classification of important elements of protein-coding genes, other genomic elements such as pseudogenes and the non-coding genome, comparative-genomic approaches for inferring gene function, and new technologies for aiding genome annotation, as a practical guide for clinicians when considering pathogenic sequence variation. Complete and accurate annotation of structure and function of genome features has the potential to reduce both false-negative (from missing annotation) and false-positive (from incorrect annotation) errors in causal variant identification in exome and genome sequences. Re-analysis of unsolved cases will be necessary as newer technology improves genome annotation, potentially improving the rate of diagnosis.
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Affiliation(s)
- Charles A Steward
- Congenica Ltd, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR, UK. .,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | | | - Berge A Minassian
- Department of Pediatrics (Neurology), University of Texas Southwestern, Dallas, TX, USA.,Program in Genetics and Genome Biology and Department of Paediatrics (Neurology), The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, WC1N 3BG, UK.,Chalfont Centre for Epilepsy, Chesham Lane, Chalfont St Peter, Buckinghamshire, SL9 0RJ, UK
| | - Adam Frankish
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jennifer Harrow
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Illumina Inc, Great Chesterford, Essex, CB10 1XL, UK
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13
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Raju PK, Satishchandra P, Nayak S, Iyer V, Sinha S, Anand A. Microtubule-associated defects caused by EFHC1
mutations in juvenile myoclonic epilepsy. Hum Mutat 2017; 38:816-826. [DOI: 10.1002/humu.23221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/21/2017] [Accepted: 03/21/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Praveen K Raju
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research; Jakkur Bangalore Karnataka India
| | | | - Sourav Nayak
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research; Jakkur Bangalore Karnataka India
| | - Vishwanathan Iyer
- Department of Neurology; National Institute of Mental Health and Neurosciences; Bangalore Karnataka India
| | - Sanjib Sinha
- Department of Neurology; National Institute of Mental Health and Neurosciences; Bangalore Karnataka India
| | - Anuranjan Anand
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research; Jakkur Bangalore Karnataka India
- Neuroscience Unit; Jawaharlal Nehru Centre for Advanced Scientific Research; Jakkur Bangalore Karnataka India
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Thounaojam R, Langbang L, Itisham K, Sobhani R, Srivastava S, Ramanujam B, Verma R, Tripathi M, Aguan K. EFHC1 mutation in Indian juvenile myoclonic epilepsy patient. Epilepsia Open 2017; 2:84-89. [PMID: 29750216 PMCID: PMC5939392 DOI: 10.1002/epi4.12037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2016] [Indexed: 12/21/2022] Open
Abstract
Objective Juvenile myoclonic epilepsy (JME) is the most common form of idiopathic generalized epilepsies (IGEs) and is genetically heterogeneous. Mutations in EFHC1 cause JME. Because about 2 million people in India are affected by JME alone, we investigated the prevalence of mutations in the EFHC1 gene in the Indian population with JME. We studied 63 patients with JME and 80 healthy controls. Methods Clinical identification of JME was evaluated using established criteria. Following clinical evaluation of the patients and confirming presence of JME, blood samples were collected from each patient and healthy individual. Subsequently, genomic DNA was extracted from the blood samples. Eleven exons of the EFHC1 gene were individually amplified by polymerase chain reaction (PCR) for each DNA sample. The PCR products were then purified and sequenced commercially. The identified DNA variants were sequenced at least twice in both the forward and reverse directions and compared with the Exome Aggregation Consortium (ExAC) database. Results We found five heterozygous and one homozygous variant. We found three novel coding variants 661C→T, 779 G →A, and 730 C→T, which lead to R221C, R260Q, and R244STOP amino acid substitutions, respectively. The coding variant 475 C→T, resulting in the amino acid substitution R159W, reported earlier as polymorphism, was also identified in both patient and control populations. Significance Detection of these three novel variants, excluding R159W, which is considered polymorphism, expands the range of possible mutations in the EFHC1 gene. The novel variants that we are reporting herein have not been mentioned before as occurring in JME patients of other ethnic population. Therefore, these novel coding variants may be confined to the Indian JME population. Further studies on the mutational spectrum of EFHC1 in a larger number of Indian JME patients concurrent with their mode of inheritance and underlying functional assays should establish whether EFHC1 could be a panethnic gene for JME.
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Affiliation(s)
- Romita Thounaojam
- Department of Biotechnology and Bioinformatics North Eastern Hill University (NEHU) Shillong India
| | - Leader Langbang
- Department of Biotechnology and Bioinformatics North Eastern Hill University (NEHU) Shillong India
| | - Kavish Itisham
- Department of Neurology Neurosciences Centre All India Institute of Medical Sciences (AIIMS) New Delhi India
| | - Roohollah Sobhani
- Department of Biotechnology and Bioinformatics North Eastern Hill University (NEHU) Shillong India
| | - Shivani Srivastava
- Department of Neurology Neurosciences Centre All India Institute of Medical Sciences (AIIMS) New Delhi India
| | - Bhargavi Ramanujam
- Department of Neurology Neurosciences Centre All India Institute of Medical Sciences (AIIMS) New Delhi India
| | - Ramesh Verma
- Department of Neurology Neurosciences Centre All India Institute of Medical Sciences (AIIMS) New Delhi India
| | - Manjari Tripathi
- Department of Neurology Neurosciences Centre All India Institute of Medical Sciences (AIIMS) New Delhi India
| | - Kripamoy Aguan
- Department of Biotechnology and Bioinformatics North Eastern Hill University (NEHU) Shillong India
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Choi H, Pack A, Elkind MSV, Longstreth WT, Ton TGN, Onchiri F. Predictors of incident epilepsy in older adults: The Cardiovascular Health Study. Neurology 2017; 88:870-877. [PMID: 28130470 DOI: 10.1212/wnl.0000000000003662] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/30/2016] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE To determine the prevalence, incidence, and predictors of epilepsy among older adults in the Cardiovascular Health Study (CHS). METHODS We analyzed data prospectively collected in CHS and merged with data from outpatient Medicare administrative claims. We identified cases with epilepsy using self-report, antiepileptic medication, hospitalization discharge ICD-9 codes, and outpatient Medicare ICD-9 codes. We used Cox proportional hazards regression to identify factors independently associated with incident epilepsy. RESULTS At baseline, 42% of the 5,888 participants were men and 84% were white. At enrollment, 3.7% (215 of 5,888) met the criteria for prevalent epilepsy. During 14 years of follow-up totaling 48,651 person-years, 120 participants met the criteria for incident epilepsy, yielding an incidence rate of 2.47 per 1,000 person-years. The period prevalence of epilepsy by the end of follow-up was 5.7% (335 of 5,888). Epilepsy incidence rates were significantly higher among blacks than nonblacks: 4.44 vs 2.17 per 1,000 person-years (p < 0.001). In multivariable analyses, risk of incident epilepsy was significantly higher among blacks compared to nonblacks (hazard ratio [HR] 4.04, 95% confidence interval [CI] 1.99-8.17), those 75 to 79 compared to those 65 to 69 years of age (HR 2.07, 95% CI 1.21-3.55), and those with history of stroke (HR 3.49, 95% CI 1.37-8.88). CONCLUSIONS Epilepsy in older adults in the United States was common. Blacks, the very old, and those with history of stroke have a higher risk of incident epilepsy. The association with race remains unexplained.
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Affiliation(s)
- Hyunmi Choi
- From the Department of Neurology (H.C., A.P., M.S.V.E.), Columbia University, New York, NY; Departments of Neurology (W.T.L.) and Epidemiology (W.T.L., F.O.), University of Washington, Seattle; Precision Health Economics (T.G.N.T.), Oakland, CA; and Seattle Children's Research Institute (F.O.), WA.
| | - Alison Pack
- From the Department of Neurology (H.C., A.P., M.S.V.E.), Columbia University, New York, NY; Departments of Neurology (W.T.L.) and Epidemiology (W.T.L., F.O.), University of Washington, Seattle; Precision Health Economics (T.G.N.T.), Oakland, CA; and Seattle Children's Research Institute (F.O.), WA
| | - Mitchell S V Elkind
- From the Department of Neurology (H.C., A.P., M.S.V.E.), Columbia University, New York, NY; Departments of Neurology (W.T.L.) and Epidemiology (W.T.L., F.O.), University of Washington, Seattle; Precision Health Economics (T.G.N.T.), Oakland, CA; and Seattle Children's Research Institute (F.O.), WA
| | - W T Longstreth
- From the Department of Neurology (H.C., A.P., M.S.V.E.), Columbia University, New York, NY; Departments of Neurology (W.T.L.) and Epidemiology (W.T.L., F.O.), University of Washington, Seattle; Precision Health Economics (T.G.N.T.), Oakland, CA; and Seattle Children's Research Institute (F.O.), WA
| | - Thanh G N Ton
- From the Department of Neurology (H.C., A.P., M.S.V.E.), Columbia University, New York, NY; Departments of Neurology (W.T.L.) and Epidemiology (W.T.L., F.O.), University of Washington, Seattle; Precision Health Economics (T.G.N.T.), Oakland, CA; and Seattle Children's Research Institute (F.O.), WA
| | - Frankline Onchiri
- From the Department of Neurology (H.C., A.P., M.S.V.E.), Columbia University, New York, NY; Departments of Neurology (W.T.L.) and Epidemiology (W.T.L., F.O.), University of Washington, Seattle; Precision Health Economics (T.G.N.T.), Oakland, CA; and Seattle Children's Research Institute (F.O.), WA
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Helbig I, Tayoun AAN. Understanding Genotypes and Phenotypes in Epileptic Encephalopathies. Mol Syndromol 2016; 7:172-181. [PMID: 27781027 DOI: 10.1159/000448530] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Epileptic encephalopathies are severe often intractable seizure disorders where epileptiform abnormalities contribute to a progressive disturbance in brain function. Often, epileptic encephalopathies start in childhood and are accompanied by developmental delay and various neurological and non-neurological comorbidities. In recent years, this concept has become virtually synonymous with a group of severe childhood epilepsies including West syndrome, Lennox-Gastaut syndrome, Dravet syndrome, and several other severe childhood epilepsies for which genetic factors are increasingly recognized. In the last 5 years, the field has seen a virtual explosion of gene discovery, raising the number of bona fide genes and possible candidate genes for epileptic encephalopathies to more than 70 genes, explaining 20-25% of all cases with severe early-onset epilepsies that had otherwise no identifiable causes. This review will focus on the phenotypic variability as a characteristic aspect of genetic epilepsies. For many genetic epilepsies, the phenotypic presentation can be broad, even in patients with identical genetic alterations. Furthermore, patients with different genetic etiologies can have seemingly similar clinical presentations, such as in Dravet syndrome. While most patients carry mutations in SCN1A, similar phenotypes can be seen in patients with mutations in PCDH19, CHD2, SCN8A, or in rare cases GABRA1 and STXBP1. In addition to the genotypic and phenotypic heterogeneity, both benign phenotypes and severe encephalopathies have been recognized in an increasing number of genetic epilepsies, raising the question whether these conditions represent a fluid continuum or distinct entities.
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Affiliation(s)
- Ingo Helbig
- Division of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa., USA; Division of Department of Neuropediatrics, Christian Albrechts University of Kiel and University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Abou Ahmad N Tayoun
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa., USA
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EFHC1 variants in juvenile myoclonic epilepsy: reanalysis according to NHGRI and ACMG guidelines for assigning disease causality. Genet Med 2016; 19:144-156. [PMID: 27467453 DOI: 10.1038/gim.2016.86] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/09/2016] [Indexed: 12/12/2022] Open
Abstract
PURPOSE EFHC1 variants are the most common mutations in inherited myoclonic and grand mal clonic-tonic-clonic (CTC) convulsions of juvenile myoclonic epilepsy (JME). We reanalyzed 54 EFHC1 variants associated with epilepsy from 17 cohorts based on National Human Genome Research Institute (NHGRI) and American College of Medical Genetics and Genomics (ACMG) guidelines for interpretation of sequence variants. METHODS We calculated Bayesian LOD scores for variants in coinheritance, unconditional exact tests and odds ratios (OR) in case-control associations, allele frequencies in genome databases, and predictions for conservation/pathogenicity. We reviewed whether variants damage EFHC1 functions, whether efhc1-/- KO mice recapitulate CTC convulsions and "microdysgenesis" neuropathology, and whether supernumerary synaptic and dendritic phenotypes can be rescued in the fly model when EFHC1 is overexpressed. We rated strengths of evidence and applied ACMG combinatorial criteria for classifying variants. RESULTS Nine variants were classified as "pathogenic," 14 as "likely pathogenic," 9 as "benign," and 2 as "likely benign." Twenty variants of unknown significance had an insufficient number of ancestry-matched controls, but ORs exceeded 5 when compared with racial/ethnic-matched Exome Aggregation Consortium (ExAC) controls. CONCLUSIONS NHGRI gene-level evidence and variant-level evidence establish EFHC1 as the first non-ion channel microtubule-associated protein whose mutations disturb R-type VDCC and TRPM2 calcium currents in overgrown synapses and dendrites within abnormally migrated dislocated neurons, thus explaining CTC convulsions and "microdysgenesis" neuropathology of JME.Genet Med 19 2, 144-156.
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Zhao Y, Shi J, Winey M, Klymkowsky MW. Identifying domains of EFHC1 involved in ciliary localization, ciliogenesis, and the regulation of Wnt signaling. Dev Biol 2016; 411:257-265. [PMID: 26783883 DOI: 10.1016/j.ydbio.2016.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/16/2015] [Accepted: 01/07/2016] [Indexed: 12/24/2022]
Abstract
EFHC1 encodes a ciliary protein that has been linked to Juvenile Myoclonic Epilepsy. In ectodermal explants, derived from Xenopus laevis embryos, the morpholino-mediated down-regulation of EFHC1b inhibited multiciliated cell formation. In those ciliated cells that did form, axoneme but not basal body formation was inhibited. EFHC1b morphant embryos displayed defects in central nervous system (CNS) and neural crest patterning that were rescued by a EFHC1b-GFP chimera. EFHC1b-GFP localized to ciliary axonemes in epidermal, gastrocoele roof plate, and neural tube cells. In X. laevis there is a link between Wnt signaling and multiciliated cell formation. While down-regulation of EFHC1b led to a ~2-fold increase in the activity of the β-catenin/Wnt-responsive TOPFLASH reporter, EFHC1b-GFP did not inhibit β-catenin activation of TOPFLASH. Wnt8a RNA levels were increased in EFHC1b morphant ectodermal explants and intact embryos, analyzed prior to the on-set of ciliogenesis. Rescue of the EFHC1b MO's ciliary axonemal phenotypes required the entire protein; in contrast, the EFHC1b morpholino's Wnt8a, CNS, and neural crest phenotypes were rescued by a truncated form of EFHC1b. The EFHC1b morpholino's Wnt8a phenotype was also rescued by the injection of RNAs encoding secreted Wnt inhibitors, suggesting that these phenotypes are due to effects on Wnt signaling, rather than the loss of cilia, an observation of potential relevance to understanding EFHC1's role in human neural development.
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Affiliation(s)
- Ying Zhao
- Molecular, Cellular & Developmental Biology, University of Colorado Boulder Boulder, Colorado 80309-0347, USA
| | - Jianli Shi
- Molecular, Cellular & Developmental Biology, University of Colorado Boulder Boulder, Colorado 80309-0347, USA
| | - Mark Winey
- Molecular, Cellular & Developmental Biology, University of Colorado Boulder Boulder, Colorado 80309-0347, USA
| | - Michael W Klymkowsky
- Molecular, Cellular & Developmental Biology, University of Colorado Boulder Boulder, Colorado 80309-0347, USA.
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