title: Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat.
abstract: Target capture sequencing is an efficient approach to directly identify the causative mutations of genetic disorders. To apply this strategy to laboratory rats exhibiting various phenotypes, we developed a novel target capture probe set, TargetEC (target capture for exons and conserved non-coding sequences), which can identify mutations not only in exonic regions but also in conserved non-coding sequences and thus can detect regulatory mutations.
  
  
  
  TargetEC covers 1,078,129 regions spanning 146.8 Mb of the genome. We applied TargetEC to four inbred rat strains (WTC/Kyo, WTC-swh/Kyo, PVG/Seac, and KFRS4/Kyo) maintained by the National BioResource Project for the Rat in Japan, and successfully identified mutations associated with these phenotypes, including one mutation detected in a conserved non-coding sequence.
  
  
  
  The method developed in this study can be used to efficiently identify regulatory mutations, which cannot be detected using conventional exome sequencing, and will help to deepen our understanding of the relationships between regulatory mutations and associated phenotypes.
authors: Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.|AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan.
authors: Minako
authors: M
authors: Yoshihara
authors: Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.|AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan.
authors: Daisuke
authors: D
authors: Saito
authors: Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.|AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan.
authors: Tetsuya
authors: T
authors: Sato
authors: Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, 292-0818, Chiba, Japan.
authors: Osamu
authors: O
authors: Ohara
authors: Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
authors: Takashi
authors: T
authors: Kuramoto
authors: Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan. mikita@bioreg.kyushu-u.ac.jp.|AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan. mikita@bioreg.kyushu-u.ac.jp.
authors: Mikita
authors: M
authors: Suyama
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D005091:Exons; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D054643:INDEL Mutation; D007438:Introns; D020641:Polymorphism, Single Nucleotide; D051381:Rats; D015203:Reproducibility of Results; D020506:Untranslated Regions
chemical_list: D020506:Untranslated Regions
keywords: Conserved non-coding sequence; Exome; Rat; Target capture sequencing