title: Targeted capture and sequencing for detection of mutations causing early onset epileptic encephalopathy.
abstract: OBJECTIVE
  Early onset epileptic encephalopathies (EOEEs) are heterogeneous epileptic disorders caused by various abnormalities in causative genes including point mutations and copy number variations (CNVs). In this study, we performed targeted capture and sequencing of a subset of genes to detect point mutations and CNVs simultaneously.
  
  
  METHODS
  We designed complementary RNA oligonucleotide probes against the coding exons of 35 known and potential candidate genes. We tested 68 unrelated patients, including 15 patients with previously detected mutations as positive controls. In addition to mutation detection by the Genome Analysis Toolkit, CNVs were detected by the relative depth of coverage ratio. All detected events were confirmed by Sanger sequencing or genomic microarray analysis.
  
  
  RESULTS
  We detected all positive control mutations. In addition, in 53 patients with EOEEs, we detected 12 pathogenic mutations, including 9 point mutations (2 nonsense, 3 splice-site, and 4 missense mutations), 2 frameshift mutations, and one 3.7-Mb microdeletion. Ten of the 12 mutations occurred de novo; the other two had been previously reported as pathogenic. The entire process of targeted capture, sequencing, and analysis required 1 week for the testing of up to 24 patients.
  
  
  CONCLUSIONS
  Targeted capture and sequencing enables the identification of mutations of all classes causing EOEEs, highlighting its usefulness for rapid and comprehensive genetic testing.
authors.affiliation: Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Kodera
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Kato
authors.forename: Alex S
authors.initials: AS
authors.lastname: Nord
authors.forename: Tom
authors.initials: T
authors.lastname: Walsh
authors.forename: Ming
authors.initials: M
authors.lastname: Lee
authors.forename: Gaku
authors.initials: G
authors.lastname: Yamanaka
authors.forename: Jun
authors.initials: J
authors.lastname: Tohyama
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Nakamura
authors.forename: Eiji
authors.initials: E
authors.lastname: Nakagawa
authors.forename: Tae
authors.initials: T
authors.lastname: Ikeda
authors.forename: Bruria
authors.initials: B
authors.lastname: Ben-Zeev
authors.forename: Dorit
authors.initials: D
authors.lastname: Lev
authors.forename: Tally
authors.initials: T
authors.lastname: Lerman-Sagie
authors.forename: Rachel
authors.initials: R
authors.lastname: Straussberg
authors.forename: Saori
authors.initials: S
authors.lastname: Tanabe
authors.forename: Kazutoshi
authors.initials: K
authors.lastname: Ueda
authors.forename: Masano
authors.initials: M
authors.lastname: Amamoto
authors.forename: Sayaka
authors.initials: S
authors.lastname: Ohta
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Nonoda
authors.forename: Kiyomi
authors.initials: K
authors.lastname: Nishiyama
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Tsurusaki
authors.forename: Mitsuko
authors.initials: M
authors.lastname: Nakashima
authors.forename: Noriko
authors.initials: N
authors.lastname: Miyake
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Hayasaka
authors.forename: Mary-Claire
authors.initials: MC
authors.lastname: King
authors.forename: Naomichi
authors.initials: N
authors.lastname: Matsumoto
authors.forename: Hirotomo
authors.initials: H
authors.lastname: Saitsu
mesh_terms: D002352:Carrier Proteins / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics*; D004569:Electroencephalography; D005260:Female; D005820:Genetic Testing; D006801:Humans; D008297:Male; D046228:Microarray Analysis; D008840:Microfilament Proteins / Q000235:genetics; D051938:Munc18 Proteins / Q000235:genetics; D009154:Mutation / Q000235:genetics*; D062550:NAV1.1 Voltage-Gated Sodium Channel / Q000235:genetics; D062551:NAV1.2 Voltage-Gated Sodium Channel / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D013036:Spasms, Infantile / Q000235:genetics*; D013049:Spectrin
chemical_list: D002352:Carrier Proteins; D008840:Microfilament Proteins; D051938:Munc18 Proteins; D062550:NAV1.1 Voltage-Gated Sodium Channel; D062551:NAV1.2 Voltage-Gated Sodium Channel; D013049:Spectrin; C568242:SCN1A protein, human; C568251:SCN2A protein, human; C497937:STXBP1 protein, human
keywords: Copy number variation; Genetic testing; Mutation; Sequencing; Target capture