Abstract
Background: 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. Results: 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. Conclusions: 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.
| Original language | English |
|---|---|
| Article number | 593 |
| Journal | BMC Genomics |
| Volume | 17 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - Aug 9 2016 |
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All Science Journal Classification (ASJC) codes
- Biotechnology
- Genetics
Cite this
Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat. / Yoshihara, Minako; Saito, Daisuke; Sato, Tetsuya; Ohara, Osamu; Kuramoto, Takashi; Suyama, Mikita.
In: BMC Genomics, Vol. 17, No. 1, 593, 09.08.2016.Research output: Contribution to journal › Article
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TY - JOUR
T1 - Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat
AU - Yoshihara, Minako
AU - Saito, Daisuke
AU - Sato, Tetsuya
AU - Ohara, Osamu
AU - Kuramoto, Takashi
AU - Suyama, Mikita
PY - 2016/8/9
Y1 - 2016/8/9
N2 - Background: 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. Results: 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. Conclusions: 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.
AB - Background: 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. Results: 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. Conclusions: 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.
UR - http://www.scopus.com/inward/record.url?scp=84988345810&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84988345810&partnerID=8YFLogxK
U2 - 10.1186/s12864-016-2975-9
DO - 10.1186/s12864-016-2975-9
M3 - Article
C2 - 27506932
AN - SCOPUS:84988345810
VL - 17
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
IS - 1
M1 - 593
ER -