title: A targeted resequencing gene panel for focal epilepsy.
abstract: OBJECTIVE
  We report development of a targeted resequencing gene panel for focal epilepsy, the most prevalent phenotypic group of the epilepsies.
  
  
  METHODS
  The targeted resequencing gene panel was designed using molecular inversion probe (MIP) capture technology and sequenced using massively parallel Illumina sequencing.
  
  
  RESULTS
  We demonstrated proof of principle that mutations can be detected in 4 previously genotyped focal epilepsy cases. We searched for both germline and somatic mutations in 251 patients with unsolved sporadic or familial focal epilepsy and identified 11 novel or very rare missense variants in 5 different genes: CHRNA4, GRIN2B, KCNT1, PCDH19, and SCN1A. Of these, 2 were predicted to be pathogenic or likely pathogenic, explaining ∼0.8% of the cohort, and 8 were of uncertain significance based on available data.
  
  
  CONCLUSIONS
  We have developed and validated a targeted resequencing panel for focal epilepsies, the most important clinical class of epilepsies, accounting for about 60% of all cases. Our application of MIP technology is an innovative approach that will be advantageous in the clinical setting because it is highly sensitive, efficient, and cost-effective for screening large patient cohorts. Our findings indicate that mutations in known genes likely explain only a small proportion of focal epilepsy cases. This is not surprising given the established clinical and genetic heterogeneity of these disorders and underscores the importance of further gene discovery studies in this complex syndrome.
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Hildebrand
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Candace T
authors.initials: CT
authors.lastname: Myers
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Gemma L
authors.initials: GL
authors.lastname: Carvill
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Brigid M
authors.initials: BM
authors.lastname: Regan
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: John A
authors.initials: JA
authors.lastname: Damiano
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Saul A
authors.initials: SA
authors.lastname: Mullen
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Mark R
authors.initials: MR
authors.lastname: Newton
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Umesh
authors.initials: U
authors.lastname: Nair
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Elena V
authors.initials: EV
authors.lastname: Gazina
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Carol J
authors.initials: CJ
authors.lastname: Milligan
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Reid
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Steven
authors.initials: S
authors.lastname: Petrou
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Ingrid E
authors.initials: IE
authors.lastname: Scheffer
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia. hmefford@uw.edu s.berkovic@unimelb.edu.au.
authors.forename: Samuel F
authors.initials: SF
authors.lastname: Berkovic
authors.affiliation: From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia. hmefford@uw.edu s.berkovic@unimelb.edu.au.
authors.forename: Heather C
authors.initials: HC
authors.lastname: Mefford
mesh_terms: D015820:Cadherins / Q000235:genetics; D015331:Cohort Studies; D004828:Epilepsies, Partial / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease; D005820:Genetic Testing / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D009154:Mutation; D062550:NAV1.1 Voltage-Gated Sodium Channel / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics; D015221:Potassium Channels / Q000235:genetics; D000081033:Potassium Channels, Sodium-Activated; D000091363:Protocadherins; D016194:Receptors, N-Methyl-D-Aspartate / Q000235:genetics; D011978:Receptors, Nicotinic / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D015820:Cadherins; D062550:NAV1.1 Voltage-Gated Sodium Channel; D009419:Nerve Tissue Proteins; D015221:Potassium Channels; D000081033:Potassium Channels, Sodium-Activated; D000091363:Protocadherins; D016194:Receptors, N-Methyl-D-Aspartate; D011978:Receptors, Nicotinic; C585122:KCNT1 protein, human; C121001:NR2B NMDA receptor; C438605:PCDH19 protein, human; C568242:SCN1A protein, human