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Fattahi Z, Kalhor Z, Fadaee M, Vazehan R, Parsimehr E, Abolhassani A, Beheshtian M, Zamani G, Nafissi S, Nilipour Y, Akbari M, Kahrizi K, Kariminejad A, Najmabadi H. Improved diagnostic yield of neuromuscular disorders applying clinical exome sequencing in patients arising from a consanguineous population. Clin Genet 2016; 91:386-402. [DOI: 10.1111/cge.12810] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Z. Fattahi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - Z. Kalhor
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - M. Fadaee
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - R. Vazehan
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - E. Parsimehr
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - A. Abolhassani
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - M. Beheshtian
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - G. Zamani
- Department of NeurologyTehran University of Medical Sciences Tehran Iran
| | - S. Nafissi
- Department of Pediatric Neurology, Pediatrics Center of Excellence, Children's Medical CenterTehran University of Medical Sciences Tehran Iran
| | - Y. Nilipour
- Pediatric Pathology Research Center, Mofid Children HospitalShahid Beheshti University of Medical Sciences Tehran Iran
| | - M.R. Akbari
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Women's College Research InstituteWomen's College Hospital Toronto Canada
- Dalla Lana School of Public HealthUniversity of Toronto Toronto Canada
| | - K. Kahrizi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - A. Kariminejad
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - H. Najmabadi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
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Hardies K, Cai Y, Jardel C, Jansen AC, Cao M, May P, Djémié T, Hachon Le Camus C, Keymolen K, Deconinck T, Bhambhani V, Long C, Sajan SA, Helbig KL, Suls A, Balling R, Helbig I, De Jonghe P, Depienne C, De Camilli P, Weckhuysen S. Loss of SYNJ1 dual phosphatase activity leads to early onset refractory seizures and progressive neurological decline. Brain 2016; 139:2420-30. [PMID: 27435091 DOI: 10.1093/brain/aww180] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/07/2016] [Indexed: 12/30/2022] Open
Abstract
SYNJ1 encodes a polyphosphoinositide phosphatase, synaptojanin 1, which contains two consecutive phosphatase domains and plays a prominent role in synaptic vesicle dynamics. Autosomal recessive inherited variants in SYNJ1 have previously been associated with two different neurological diseases: a recurrent homozygous missense variant (p.Arg258Gln) that abolishes Sac1 phosphatase activity was identified in three independent families with early onset parkinsonism, whereas a homozygous nonsense variant (p.Arg136*) causing a severe decrease of mRNA transcript was found in a single patient with intractable epilepsy and tau pathology. We performed whole exome or genome sequencing in three independent sib pairs with early onset refractory seizures and progressive neurological decline, and identified novel segregating recessive SYNJ1 defects. A homozygous missense variant resulting in an amino acid substitution (p.Tyr888Cys) was found to impair, but not abolish, the dual phosphatase activity of SYNJ1, whereas three premature stop variants (homozygote p.Trp843* and compound heterozygote p.Gln647Argfs*6/p.Ser1122Thrfs*3) almost completely abolished mRNA transcript production. A genetic follow-up screening in a large cohort of 543 patients with a wide phenotypical range of epilepsies and intellectual disability revealed no additional pathogenic variants, showing that SYNJ1 deficiency is rare and probably linked to a specific phenotype. While variants leading to early onset parkinsonism selectively abolish Sac1 function, our results provide evidence that a critical reduction of the dual phosphatase activity of SYNJ1 underlies a severe disorder with neonatal refractory epilepsy and a neurodegenerative disease course. These findings further expand the clinical spectrum of synaptic dysregulation in patients with severe epilepsy, and emphasize the importance of this biological pathway in seizure pathophysiology.
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Meisler MH, Helman G, Hammer MF, Fureman BE, Gaillard WD, Goldin AL, Hirose S, Ishii A, Kroner BL, Lossin C, Mefford HC, Parent JM, Patel M, Schreiber J, Stewart R, Whittemore V, Wilcox K, Wagnon JL, Pearl PL, Vanderver A, Scheffer IE. SCN8A encephalopathy: Research progress and prospects. Epilepsia 2016; 57:1027-35. [PMID: 27270488 PMCID: PMC5495462 DOI: 10.1111/epi.13422] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2016] [Indexed: 01/15/2023]
Abstract
On April 21, 2015, the first SCN8A Encephalopathy Research Group convened in Washington, DC, to assess current research into clinical and pathogenic features of the disorder and prepare an agenda for future research collaborations. The group comprised clinical and basic scientists and representatives of patient advocacy groups. SCN8A encephalopathy is a rare disorder caused by de novo missense mutations of the sodium channel gene SCN8A, which encodes the neuronal sodium channel Nav 1.6. Since the initial description in 2012, approximately 140 affected individuals have been reported in publications or by SCN8A family groups. As a result, an understanding of the severe impact of SCN8A mutations is beginning to emerge. Defining a genetic epilepsy syndrome goes beyond identification of molecular etiology. Topics discussed at this meeting included (1) comparison between mutations of SCN8A and the SCN1A mutations in Dravet syndrome, (2) biophysical properties of the Nav 1.6 channel, (3) electrophysiologic effects of patient mutations on channel properties, (4) cell and animal models of SCN8A encephalopathy, (5) drug screening strategies, (6) the phenotypic spectrum of SCN8A encephalopathy, and (7) efforts to develop a bioregistry. A panel discussion of gaps in bioregistry, biobanking, and clinical outcomes data was followed by a planning session for improved integration of clinical and basic science research. Although SCN8A encephalopathy was identified only recently, there has been rapid progress in functional analysis and phenotypic classification. The focus is now shifting from identification of the underlying molecular cause to the development of strategies for drug screening and prioritized patient care.
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Affiliation(s)
- Miriam H. Meisler
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, U.S.A
| | - Guy Helman
- Department of Neurology, Children’s National Health System, Washington, District of Columbia, U.S.A
- Center for Genetic Medicine Research, Children’s National Health System, Washington, District of Columbia, U.S.A
| | - Michael F. Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, U.S.A
| | - Brandy E. Fureman
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - William D. Gaillard
- Department of Neurology, Children’s National Health System, Washington, District of Columbia, U.S.A
- Center for Neuroscience Research, Children’s National Health System, Washington, District of Columbia, U.S.A
| | - Alan L. Goldin
- Microbiology & Molecular Genetics and Anatomy & Neurobiology, University of California, Irvine, California, U.S.A
| | - Shinichi Hirose
- Department of Pediatrics, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Atsushi Ishii
- Department of Pediatrics, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Barbara L. Kroner
- Biostatistics and Epidemiology, RTI International, Rockville, Maryland, U.S.A
| | - Christoph Lossin
- Department of Neurology, School of Medicine, University of California Davis, Sacramento, California, U.S.A
| | - Heather C. Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, U.S.A
| | - Jack M. Parent
- Department of Neurology, University of Michigan Medical Center and VA Ann Arbor Healthcare System, Ann Arbor, Michigan, U.S.A
| | - Manoj Patel
- Department of Anesthesiology, University of Virginia Health System, Charlottesville, Virginia, U.S.A
| | - John Schreiber
- Department of Neurology, Children’s National Health System, Washington, District of Columbia, U.S.A
| | - Randall Stewart
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Vicky Whittemore
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Karen Wilcox
- Anticonvulsant Drug Development Program, Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, U.S.A
| | - Jacy L Wagnon
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, U.S.A
| | - Phillip L. Pearl
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, U.S.A
| | - Adeline Vanderver
- Department of Neurology, Children’s National Health System, Washington, District of Columbia, U.S.A
- Center for Genetic Medicine Research, Children’s National Health System, Washington, District of Columbia, U.S.A
- Department of Integrated Systems Biology and Pediatrics, George Washington University, Washington, District of Columbia, U.S.A
| | - Ingrid E. Scheffer
- Department of Neurology, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Florey Institute of Neurosciences and Mental Health, Melbourne, Victoria, Australia
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Reducing the Cost of the Diagnostic Odyssey in Early Onset Epileptic Encephalopathies. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6421039. [PMID: 27243033 PMCID: PMC4875968 DOI: 10.1155/2016/6421039] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/26/2016] [Accepted: 04/07/2016] [Indexed: 11/25/2022]
Abstract
Whole exome sequencing (WES) has revolutionized the way we think about and diagnose epileptic encephalopathies. Multiple recent review articles discuss the benefits of WES and suggest various algorithms to follow for determining the etiology of epileptic encephalopathies. Incorporation of WES in these algorithms is leading to the discovery of new genetic diagnoses of early onset epileptic encephalopathies (EOEEs) at a rapid rate; however, WES is not yet a universally utilized diagnostic tool. Clinical WES may be underutilized due to provider discomfort in ordering the test or perceived costliness. At our hospital WES is not routinely performed for patients with EOEE due to limited insurance reimbursement. In fact for any patient with noncommercial insurance (Medicaid) the institution does not allow sending out WES as this is not “established”/“proven to be highly useful and cost effective”/“approved test” in patients with epilepsy. Recently, we performed WES on four patients from three families and identified novel mutations in known epilepsy genes in all four cases. These patients had State Medicaid as their insurance carrier and were followed up for several years for EOEE while being worked up using the traditional/approved testing methods. Following a recently proposed diagnostic pathway, we analyzed the cost savings (US dollars) that could be accrued if WES was performed earlier in the diagnostic odyssey. This is the first publication that addresses the dollar cost of traditional testing in EOEE as performed in these four cases versus WES and the potential cost savings.
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Genetic Testing in Epileptic Encephalopathy: Rosetta Stone or Just an Expensive Rock? Epilepsy Curr 2016; 16:12-3. [DOI: 10.5698/1535-7597-16.1.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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56
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Myers C, Mefford H. Genetic investigations of the epileptic encephalopathies. PROGRESS IN BRAIN RESEARCH 2016; 226:35-60. [DOI: 10.1016/bs.pbr.2016.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wagnon JL, Barker BS, Hounshell JA, Haaxma CA, Shealy A, Moss T, Parikh S, Messer RD, Patel MK, Meisler MH. Pathogenic mechanism of recurrent mutations of SCN8A in epileptic encephalopathy. Ann Clin Transl Neurol 2015; 3:114-23. [PMID: 26900580 PMCID: PMC4748308 DOI: 10.1002/acn3.276] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/20/2015] [Indexed: 12/03/2022] Open
Abstract
Objective The early infantile epileptic encephalopathy type 13 (EIEE13, OMIM #614558) results from de novo missense mutations of SCN8A encoding the voltage‐gated sodium channel Nav1.6. More than 20% of patients have recurrent mutations in residues Arg1617 or Arg1872. Our goal was to determine the functional effects of these mutations on channel properties. Methods Clinical exome sequencing was carried out on patients with early‐onset seizures, developmental delay, and cognitive impairment. Two mutations identified here, p.Arg1872Leu and p.Arg1872Gln, and two previously identified mutations, p.Arg1872Trp and p.Arg1617Gln, were introduced into Nav1.6 cDNA, and effects on electrophysiological properties were characterized in transfected ND7/23 cells. Interactions with FGF14, G‐protein subunit Gβγ, and sodium channel subunit β1 were assessed by coimmunoprecipitation. Results We identified two patients with the novel mutation p.Arg1872Leu and one patient with the recurrent mutation p.Arg1872Gln. The three mutations of Arg1872 and the mutation of Arg1617 all impaired the sodium channel transition from open state to inactivated state, resulting in channel hyperactivity. Other observed abnormalities contributing to elevated channel activity were increased persistent current, increased peak current density, hyperpolarizing shift in voltage dependence of activation, and depolarizing shift in steady‐state inactivation. Protein interactions were not affected. Interpretation Recurrent mutations at Arg1617 and Arg1872 lead to elevated Nav1.6 channel activity by impairing channel inactivation. Channel hyperactivity is the major pathogenic mechanism for gain‐of‐function mutations of SCN8A. EIEE13 differs mechanistically from Dravet syndrome, which is caused by loss‐of‐function mutations of SCN1A. This distinction has important consequences for selection of antiepileptic drugs and the development of gene‐ and mutation‐specific treatments.
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Affiliation(s)
- Jacy L Wagnon
- Department of Human Genetics University of Michigan Ann Arbor Michigan
| | - Bryan S Barker
- Department of Anesthesiology and Neuroscience Graduate Program University of Virginia Health System Charlottesville Virginia
| | - James A Hounshell
- Department of Anesthesiology and Neuroscience Graduate Program University of Virginia Health System Charlottesville Virginia
| | - Charlotte A Haaxma
- Department of Pediatric Neurology Radboud University Nijmegen The Netherlands
| | - Amy Shealy
- Cleveland Clinic Genomic Medicine Institute Cleveland Ohio
| | - Timothy Moss
- Cleveland Clinic Genomic Medicine Institute Cleveland Ohio
| | - Sumit Parikh
- Department of Pediatric Neurology Cleveland Clinic Cleveland Ohio
| | - Ricka D Messer
- Department of Pediatric Neurology Johns Hopkins Medical Institute Baltimore Maryland
| | - Manoj K Patel
- Department of Anesthesiology and Neuroscience Graduate Program University of Virginia Health System Charlottesville Virginia
| | - Miriam H Meisler
- Department of Human Genetics University of Michigan Ann Arbor Michigan
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Human genotype–phenotype databases: aims, challenges and opportunities. Nat Rev Genet 2015; 16:702-15. [DOI: 10.1038/nrg3932] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Sawyer SL, Hartley T, Dyment DA, Beaulieu CL, Schwartzentruber J, Smith A, Bedford HM, Bernard G, Bernier FP, Brais B, Bulman DE, Warman Chardon J, Chitayat D, Deladoëy J, Fernandez BA, Frosk P, Geraghty MT, Gerull B, Gibson W, Gow RM, Graham GE, Green JS, Heon E, Horvath G, Innes AM, Jabado N, Kim RH, Koenekoop RK, Khan A, Lehmann OJ, Mendoza-Londono R, Michaud JL, Nikkel SM, Penney LS, Polychronakos C, Richer J, Rouleau GA, Samuels ME, Siu VM, Suchowersky O, Tarnopolsky MA, Yoon G, Zahir FR, Majewski J, Boycott KM. Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care. Clin Genet 2015; 89:275-84. [PMID: 26283276 PMCID: PMC5053223 DOI: 10.1111/cge.12654] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/14/2015] [Accepted: 08/14/2015] [Indexed: 12/17/2022]
Abstract
An accurate diagnosis is an integral component of patient care for children with rare genetic disease. Recent advances in sequencing, in particular whole‐exome sequencing (WES), are identifying the genetic basis of disease for 25–40% of patients. The diagnostic rate is probably influenced by when in the diagnostic process WES is used. The Finding Of Rare Disease GEnes (FORGE) Canada project was a nation‐wide effort to identify mutations for childhood‐onset disorders using WES. Most children enrolled in the FORGE project were toward the end of the diagnostic odyssey. The two primary outcomes of FORGE were novel gene discovery and the identification of mutations in genes known to cause disease. In the latter instance, WES identified mutations in known disease genes for 105 of 362 families studied (29%), thereby informing the impact of WES in the setting of the diagnostic odyssey. Our analysis of this dataset showed that these known disease genes were not identified prior to WES enrollment for two key reasons: genetic heterogeneity associated with a clinical diagnosis and atypical presentation of known, clinically recognized diseases. What is becoming increasingly clear is that WES will be paradigm altering for patients and families with rare genetic diseases.
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Affiliation(s)
- S L Sawyer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - T Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - C L Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | - A Smith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - H M Bedford
- Genetics Program, North York General Hospital, Toronto, Canada
| | - G Bernard
- Departments of Pediatrics, Neurology and Neurosurgery, Division of Pediatric Neurology, Montréal Children's Hospital, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - F P Bernier
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - B Brais
- Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | - D Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - J Deladoëy
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - B A Fernandez
- Disciplines of Genetics and Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - P Frosk
- Departments of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada
| | - M T Geraghty
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - B Gerull
- Cardiac Sciences and Medical Genetics, University of Calgary, Calgary, Canada
| | - W Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - R M Gow
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - G E Graham
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J S Green
- Disciplines of Genetics and Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - E Heon
- Department of Ophthalmology and Vision Sciences, Program of Genetics and Genomic Biology, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - G Horvath
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - A M Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - N Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - R H Kim
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada.,Department of Medicine, University of Toronto, Toronto, Canada
| | - R K Koenekoop
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Canada
| | - A Khan
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - O J Lehmann
- Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, Canada
| | - R Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - J L Michaud
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - S M Nikkel
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - L S Penney
- Medical Genetics, IWK Health Centre, Halifax, Canada
| | - C Polychronakos
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - J Richer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - G A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - M E Samuels
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - V M Siu
- Division of Medical Genetics, Department of Pediatrics, University of Western Ontario, London, Canada
| | - O Suchowersky
- Departments of Medicine, Medical Genetics, and Pediatrics, University of Alberta, Edmonton, Canada
| | - M A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - G Yoon
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - F R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | | | - J Majewski
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
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Abstract
Epilepsy is a group of disorders characterized by recurrent seizures, and is one of the most common neurological conditions. The genetic basis of epilepsy is clear from epidemiological studies and from rare gene discoveries in large families. The three major classes of epilepsy disorders are genetic generalized, focal and encephalopathic epilepsies, with several specific disorders within each class. Advances in genomic technologies that facilitate genome-wide discovery of both common and rare variants have led to a rapid increase in our understanding of epilepsy genetics. Copy number variant and genome-wide association studies have contributed to our understanding of the complex genetic architecture of generalized epilepsy, while genetic insights into the focal epilepsies and epileptic encephalopathies have come primarily from exome sequencing. It is increasingly clear that epilepsy is genetically heterogeneous, and novel gene discoveries have moved the field beyond the known contribution of ion channels to implicate chromatin remodeling, transcriptional regulation and regulation of the mammalian target of rapamycin (mTOR) protein in the etiology of epilepsy. Such discoveries pave the way for new therapeutics, some of which are already being studied. In this review, we discuss the rapid pace of gene discovery in epilepsy, as facilitated by genomic technologies, and highlight several novel genes and potential therapies.
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Affiliation(s)
- Candace T Myers
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA.
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Delineation of New Disorders and Phenotypic Expansion of Known Disorders Through Whole Exome Sequencing. CURRENT GENETIC MEDICINE REPORTS 2015. [DOI: 10.1007/s40142-015-0079-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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van den Veyver IB, Eng CM. Genome-Wide Sequencing for Prenatal Detection of Fetal Single-Gene Disorders. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a023077. [PMID: 26253094 DOI: 10.1101/cshperspect.a023077] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
New sequencing methods capable of rapidly analyzing the genome at increasing resolution have transformed diagnosis of single-gene or oligogenic genetic disorders in pediatric and adult medicine. Targeted tests, consisting of disease-focused multigene panels and diagnostic exome sequencing to interrogate the sequence of the coding regions of nearly all genes, are now clinically offered when there is suspicion for an undiagnosed genetic disorder or cancer in children and adults. Implementation of diagnostic exome and genome sequencing tests on invasively and noninvasively obtained fetal DNA samples for prenatal genetic diagnosis is also being explored. We predict that they will become more widely integrated into prenatal care in the near future. Providers must prepare for the practical, ethical, and societal dilemmas that accompany the capacity to generate and analyze large amounts of genetic information about the fetus during pregnancy.
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Affiliation(s)
- Ignatia B van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, The Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
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Smedley D, Robinson PN. Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. Genome Med 2015; 7:81. [PMID: 26229552 PMCID: PMC4520011 DOI: 10.1186/s13073-015-0199-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Whole exome sequencing has altered the way in which rare diseases are diagnosed and disease genes identified. Hundreds of novel disease-associated genes have been characterized by whole exome sequencing in the past five years, yet the identification of disease-causing mutations is often challenging because of the large number of rare variants that are being revealed. Gene prioritization aims to rank the most probable candidate genes towards the top of a list of potentially pathogenic variants. A promising new approach involves the computational comparison of the phenotypic abnormalities of the individual being investigated with those previously associated with human diseases or genetically modified model organisms. In this review, we compare and contrast the strengths and weaknesses of current phenotype-driven computational algorithms, including Phevor, Phen-Gen, eXtasy and two algorithms developed by our groups called PhenIX and Exomiser. Computational phenotype analysis can substantially improve the performance of exome analysis pipelines.
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Affiliation(s)
- Damian Smedley
- />Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter N. Robinson
- />Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- />Max Planck Institute for Molecular Genetics, Ihnestrasse, 14195 Berlin, Germany
- />Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz, 13353 Berlin, Germany
- />Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse, 14195 Berlin, Germany
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Parker MJ, Fryer AE, Shears DJ, Lachlan KL, McKee SA, Magee AC, Mohammed S, Vasudevan PC, Park SM, Benoit V, Lederer D, Maystadt I, Study D, FitzPatrick DR. De novo, heterozygous, loss-of-function mutations in SYNGAP1 cause a syndromic form of intellectual disability. Am J Med Genet A 2015; 167A:2231-7. [PMID: 26079862 PMCID: PMC4744742 DOI: 10.1002/ajmg.a.37189] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/11/2015] [Indexed: 01/27/2023]
Abstract
De novo mutations (DNM) in SYNGAP1, encoding Ras/Rap GTPase‐activating protein SynGAP, have been reported in individuals with nonsyndromic intellectual disability (ID). We identified 10 previously unreported individuals with SYNGAP1 DNM; seven via the Deciphering Developmental Disorders (DDD) Study, one through clinical analysis for copy number variation and the remaining two (monozygotic twins) via a research multi‐gene panel analysis. Seven of the nine heterozygous mutations are likely to result in loss‐of‐function (3 nonsense; 3 frameshift; 1 whole gene deletion). The remaining two mutations, one of which affected the monozygotic twins, were missense variants. Each individual carrying a DNM in SYNGAP1 had moderate‐to‐severe ID and 7/10 had epilepsy; typically myoclonic seizures, absences or drop attacks. 8/10 had hypotonia, 5/10 had significant constipation, 7/10 had wide‐based/unsteady gait, 3/10 had strabismus, and 2/10 had significant hip dysplasia. A proportion of the affected individuals had a similar, myopathic facial appearance, with broad nasal bridge, relatively long nose and full lower lip vermilion. A distinctive behavioral phenotype was also observed with aggressive/challenging behavior and significant sleep problems being common. 7/10 individuals had MR imaging of the brain each of which was reported as normal. The clinical features of the individuals reported here show significant overlap with those associated with 6p21.3 microdeletions, confirming that haploinsufficiency for SYNGAP1 is responsible for both disorders. © 2015 The Authors. American Journal of Medical Genetics Part A Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Michael J Parker
- Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield, UK
| | - Alan E Fryer
- Clinical Genetics Department, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Deborah J Shears
- Department of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Katherine L Lachlan
- Wessex Clinical Genetics Service, University Hospitals Southampton, Southampton, UK.,Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Shane A McKee
- Department of Genetic Medicine, Belfast City Hospital, Belfast, UK
| | - Alex C Magee
- Department of Genetic Medicine, Belfast City Hospital, Belfast, UK
| | - Shehla Mohammed
- Department of Clinical Genetics, Guy's and St. Thomas' Hospital NHS Trust, London, UK
| | - Pradeep C Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK
| | - Soo-Mi Park
- East Anglian Medical Genetics Service, Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Valérie Benoit
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique (I.P.G.), Gosselies (Charleroi), Belgium
| | - Damien Lederer
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique (I.P.G.), Gosselies (Charleroi), Belgium
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique (I.P.G.), Gosselies (Charleroi), Belgium
| | - Ddd Study
- DDD Study, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (I.G.M.M.), University of Edinburgh, UK
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65
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Wagnon JL, Meisler MH. Recurrent and Non-Recurrent Mutations of SCN8A in Epileptic Encephalopathy. Front Neurol 2015; 6:104. [PMID: 26029160 PMCID: PMC4432670 DOI: 10.3389/fneur.2015.00104] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 04/27/2015] [Indexed: 01/03/2023] Open
Abstract
Mutations of the voltage-gated sodium channel SCN8A have been identified in approximately 1% of nearly 1,500 children with early-infantile epileptic encephalopathies (EIEE) who have been tested by DNA sequencing. EIEE caused by mutation of SCN8A is designated EIEE13 (OMIM #614558). Affected children have seizure onset before 18 months of age as well as developmental and cognitive disabilities, movement disorders, and a high incidence of sudden death (SUDEP). EIEE13 is caused by de novo missense mutations of evolutionarily conserved residues in the Nav1.6 channel protein. One-third of the mutations are recurrent, and many occur at CpG dinucleotides. In this review, we discuss the effect of pathogenic mutations on the structure of the channel protein, the rate of recurrent mutation, and changes in channel function underlying this devastating disorder.
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Affiliation(s)
- Jacy L Wagnon
- Department of Human Genetics, University of Michigan , Ann Arbor, MI , USA
| | - Miriam H Meisler
- Department of Human Genetics, University of Michigan , Ann Arbor, MI , USA
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66
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Mercimek-Mahmutoglu S, Patel J, Cordeiro D, Hewson S, Callen D, Donner EJ, Hahn CD, Kannu P, Kobayashi J, Minassian BA, Moharir M, Siriwardena K, Weiss SK, Weksberg R, Snead OC. Diagnostic yield of genetic testing in epileptic encephalopathy in childhood. Epilepsia 2015; 56:707-16. [PMID: 25818041 DOI: 10.1111/epi.12954] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2015] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Epilepsy is a common neurologic disorder of childhood. To determine the genetic diagnostic yield in epileptic encephalopathy, we performed a retrospective cohort study in a single epilepsy genetics clinic. METHODS We included all patients with intractable epilepsy, global developmental delay, and cognitive dysfunction seen between January 2012 and June 2014 in the Epilepsy Genetics Clinic. Electronic patient charts were reviewed for clinical features, neuroimaging, biochemical investigations, and molecular genetic investigations including targeted next-generation sequencing of epileptic encephalopathy genes. RESULTS Genetic causes were identified in 28% of the 110 patients: 7% had inherited metabolic disorders including pyridoxine dependent epilepsy caused by ALDH7A1 mutation, Menkes disease, pyridox(am)ine-5-phosphate oxidase deficiency, cobalamin G deficiency, methylenetetrahydrofolate reductase deficiency, glucose transporter 1 deficiency, glycine encephalopathy, and pyruvate dehydrogenase complex deficiency; 21% had other genetic causes including genetic syndromes, pathogenic copy number variants on array comparative genomic hybridization, and epileptic encephalopathy related to mutations in the SCN1A, SCN2A, SCN8A, KCNQ2, STXBP1, PCDH19, and SLC9A6 genes. Forty-five percent of patients obtained a genetic diagnosis by targeted next-generation sequencing epileptic encephalopathy panels. It is notable that 4.5% of patients had a treatable inherited metabolic disease. SIGNIFICANCE To the best of our knowledge, this is the first study to combine inherited metabolic disorders and other genetic causes of epileptic encephalopathy. Targeted next-generation sequencing panels increased the genetic diagnostic yield from <10% to >25% in patients with epileptic encephalopathy.
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Affiliation(s)
- Saadet Mercimek-Mahmutoglu
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jaina Patel
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Dawn Cordeiro
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Stacy Hewson
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David Callen
- Division of Neurology, Department of Pediatrics, McMaster Children's Hospital, McMaster University, Hamilton, Ontario, Canada
| | - Elizabeth J Donner
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Cecil D Hahn
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Peter Kannu
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jeff Kobayashi
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Berge A Minassian
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.,University of Toronto Michael Bahen Chair in Epilepsy Research, Toronto, Ontario, Canada
| | - Mahendranath Moharir
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Komudi Siriwardena
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Shelly K Weiss
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - O Carter Snead
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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67
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Wagnon JL, Korn MJ, Parent R, Tarpey TA, Jones JM, Hammer MF, Murphy GG, Parent JM, Meisler MH. Convulsive seizures and SUDEP in a mouse model of SCN8A epileptic encephalopathy. Hum Mol Genet 2014; 24:506-15. [PMID: 25227913 PMCID: PMC4275076 DOI: 10.1093/hmg/ddu470] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
De novo mutations of the voltage-gated sodium channel gene SCN8A have recently been recognized as a cause of epileptic encephalopathy, which is characterized by refractory seizures with developmental delay and cognitive disability. We previously described the heterozygous SCN8A missense mutation p.Asn1768Asp in a child with epileptic encephalopathy that included seizures, ataxia, and sudden unexpected death in epilepsy (SUDEP). The mutation results in increased persistent sodium current and hyperactivity of transfected neurons. We have characterized a knock-in mouse model expressing this dominant gain-of-function mutation to investigate the pathology of the altered channel in vivo. The mutant channel protein is stable in vivo. Heterozygous Scn8aN1768D/+ mice exhibit seizures and SUDEP, confirming the causality of the de novo mutation in the proband. Using video/EEG analysis, we detect ictal discharges that coincide with convulsive seizures and myoclonic jerks. Prior to seizure onset, heterozygous mutants are not defective in motor learning or fear conditioning, but do exhibit mild impairment of motor coordination and social discrimination. Homozygous mutant mice exhibit earlier seizure onset than heterozygotes and more rapid progression to death. Analysis of the intermediate phenotype of functionally hemizygous Scn8aN1768D/− mice indicates that severity is increased by a double dose of mutant protein and reduced by the presence of wild-type protein. Scn8aN1768D mutant mice provide a model of epileptic encephalopathy that will be valuable for studying the in vivo effects of hyperactive Nav1.6 and the response to therapeutic interventions.
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Affiliation(s)
| | | | - Rachel Parent
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Taylor A Tarpey
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Michael F Hammer
- Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, AZ, USA
| | - Geoffrey G Murphy
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA Molecular and Integrative Physiology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA and
| | - Jack M Parent
- Department of Neurology VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
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