Abstract
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.
| Original language | English |
|---|---|
| Article number | e0200170 |
| Journal | PloS one |
| Volume | 13 |
| Issue number | 7 |
| DOIs | |
| Publication status | Published - Jul 2018 |
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All Science Journal Classification (ASJC) codes
- Biochemistry, Genetics and Molecular Biology(all)
- Agricultural and Biological Sciences(all)
Cite this
A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes. / Koganebuchi, Kae; Gakuhari, Takashi; Takeshima, Hirohiko; Sato, Kimitoshi; Fujii, Kiyotaka; Kumabe, Toshihiro; Kasagi, Satoshi; Sato, Takehiro; Tajima, Atsushi; Shibata, Hiroki; Ogawa, Motoyuki; Oota, Hiroki.
In: PloS one, Vol. 13, No. 7, e0200170, 07.2018.Research output: Contribution to journal › Article
}
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
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.
UR - http://www.scopus.com/inward/record.url?scp=85049759496&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85049759496&partnerID=8YFLogxK
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 -