A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes

PloS One
Kae KoganebuchiHiroki Oota

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.

References

Sep 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·H ShizuyaM Simon
Mar 10, 2001·Nature·V G CheungUNKNOWN BAC Resource Consortium
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jul 18, 2009·Science·Adrian W BriggsSvante Pääbo
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Jun 23, 2010·Genome Biology·Matthew N BainbridgeRichard A Gibbs
Apr 12, 2011·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Jun ZhangGenfa Zhang
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Nov 30, 2011·Nature Reviews. Genetics·Todd J Treangen, Steven L Salzberg
Feb 27, 2014·American Journal of Human Genetics·Meredith L CarpenterCarlos D Bustamante
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel

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Citations

May 21, 2021·Annals of Human Genetics·Kae KoganebuchiHiroki Oota

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Methods Mentioned

BETA
targeted capture
PCR
electrophoresis
454 Sequencing
PCRs
genotyping

Software Mentioned

SeqCap EZ
Picard
Wheeler Aligner ( BWA )
Burrows
Ensembl
GATK
SAMtools
GenotypeGVCFs
Trimmomatic
IndelRealigner

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