Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat

BMC Genomics

Methodology Article

Osamu Ohara¹  Takashi Kuramoto²  Mikita Suyama³  Daisuke Saito³  Minako Yoshihara³  Tetsuya Sato³ 

[1] Department of Technology Development, Kazusa DNA Research Institute, 292-0818, Kisarazu, Chiba, Japan;Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, 606-8501, Kyoto, Japan;Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, 812-8582, Fukuoka, Japan;AMED-CREST, Japan Agency for Medical Research and Development, 812-8582, Fukuoka, Japan;

关键词: Target capture sequencing;    Exome;    Conserved non-coding sequence;    Rat;   

DOI  :  10.1186/s12864-016-2975-9

 received in 2016-04-08, accepted in 2016-07-28,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundTarget 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.ResultsTargetEC 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2016