TY - JOUR
T1 - A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes
AU - Koganebuchi, Kae
AU - Gakuhari, Takashi
AU - Takeshima, Hirohiko
AU - Sato, Kimitoshi
AU - Fujii, Kiyotaka
AU - Kumabe, Toshihiro
AU - Kasagi, Satoshi
AU - Sato, Takehiro
AU - Tajima, Atsushi
AU - Shibata, Hiroki
AU - Ogawa, Motoyuki
AU - Oota, Hiroki
N1 - Funding Information:
This work was supported by KAKENHI (https://www.jsps.go.jp/j-grantsinaid/, Grants-in-Aid for Scientific Research B and A) to HO (25284157 and 18H03593, respectively) from the Japan Society for the Promotion of Science (JSPS). KK was supported by the JSPS Fellowship (https://www.jsps.go.jp/j-pd/, 15J10824). This work was partly performed in the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University (http://www. bioreg.kyushu-u.ac.jp/mib/activities_collabo_j. html). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Publisher Copyright:
© 2018 Koganebuchi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2018/7
Y1 - 2018/7
N2 - To analyze a specific genome region using next-generation sequencing technologies, the enrichment of DNA libraries with targeted capture methods has been standardized. For enrichment of mitochondrial genome, a previous study developed an original targeted capture method that use baits constructed from long-range polymerase chain reaction (PCR) amplicons, common laboratory reagents, and equipment. In this study, a new targeted capture method is presented, that of bacterial artificial chromosome (BAC) double capture (BDC), modifying the previous method, but using BAC libraries as baits for sequencing a relatively large gene. We applied the BDC approach for the 214 kb autosomal region, ring finger protein 213, which is the susceptibility gene of moyamoya disease (MMD). To evaluate the reliability of BDC, cost and data quality were compared with those of a commercial kit. While the ratio of duplicate reads was higher, the cost was less than that of the commercial kit. The data quality was sufficiently the same as that of the kit. Thus, BDC can be an easy, low-cost, and useful method for analyzing individual genome regions with substantial length.
AB - To analyze a specific genome region using next-generation sequencing technologies, the enrichment of DNA libraries with targeted capture methods has been standardized. For enrichment of mitochondrial genome, a previous study developed an original targeted capture method that use baits constructed from long-range polymerase chain reaction (PCR) amplicons, common laboratory reagents, and equipment. In this study, a new targeted capture method is presented, that of bacterial artificial chromosome (BAC) double capture (BDC), modifying the previous method, but using BAC libraries as baits for sequencing a relatively large gene. We applied the BDC approach for the 214 kb autosomal region, ring finger protein 213, which is the susceptibility gene of moyamoya disease (MMD). To evaluate the reliability of BDC, cost and data quality were compared with those of a commercial kit. While the ratio of duplicate reads was higher, the cost was less than that of the commercial kit. The data quality was sufficiently the same as that of the kit. Thus, BDC can be an easy, low-cost, and useful method for analyzing individual genome regions with substantial length.
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U2 - 10.1371/journal.pone.0200170
DO - 10.1371/journal.pone.0200170
M3 - Article
C2 - 30001370
AN - SCOPUS:85049759496
VL - 13
JO - PLoS One
JF - PLoS One
SN - 1932-6203
IS - 7
M1 - e0200170
ER -