Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene

Transgenic animals are extensively used to model human disease. Typically, the transgene copy number is estimated, but the exact integration site and configuration of the foreign DNA remains uncharacterized. When transgenes have been closely examined, some unexpected configurations have been found....

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Main Authors:	DuBose, Amanda J., Lichtenstein, Stephen T., Narisu, Narisu, Bonnycastle, Lori L., Swift, Amy J., Chines, Peter S., Collins, Francis S.
Format:	Online
Language:	English
Published:	Oxford University Press 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616733/

id	pubmed-3616733
recordtype	oai_dc
spelling	pubmed-36167332013-04-04 Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene DuBose, Amanda J. Lichtenstein, Stephen T. Narisu, Narisu Bonnycastle, Lori L. Swift, Amy J. Chines, Peter S. Collins, Francis S. Methods Online Transgenic animals are extensively used to model human disease. Typically, the transgene copy number is estimated, but the exact integration site and configuration of the foreign DNA remains uncharacterized. When transgenes have been closely examined, some unexpected configurations have been found. Here, we describe a method to recover transgene insertion sites and assess structural rearrangements of host and transgene DNA using microarray hybridization and targeted sequence capture. We used information about the transgene insertion site to develop a polymerase chain reaction genotyping assay to distinguish heterozygous from homozygous transgenic animals. Although we worked with a bacterial artificial chromosome transgenic mouse line, this method can be used to analyse the integration site and configuration of any foreign DNA in a sequenced genome. Oxford University Press 2013-04 2013-01-10 /pmc/articles/PMC3616733/ /pubmed/23314155 http://dx.doi.org/10.1093/nar/gks1463 Text en Published by Oxford University Press 2013. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	DuBose, Amanda J. Lichtenstein, Stephen T. Narisu, Narisu Bonnycastle, Lori L. Swift, Amy J. Chines, Peter S. Collins, Francis S.
spellingShingle	DuBose, Amanda J. Lichtenstein, Stephen T. Narisu, Narisu Bonnycastle, Lori L. Swift, Amy J. Chines, Peter S. Collins, Francis S. Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene
author_facet	DuBose, Amanda J. Lichtenstein, Stephen T. Narisu, Narisu Bonnycastle, Lori L. Swift, Amy J. Chines, Peter S. Collins, Francis S.
author_sort	DuBose, Amanda J.
title	Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene
title_short	Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene
title_full	Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene
title_fullStr	Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene
title_full_unstemmed	Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene
title_sort	use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene
description	Transgenic animals are extensively used to model human disease. Typically, the transgene copy number is estimated, but the exact integration site and configuration of the foreign DNA remains uncharacterized. When transgenes have been closely examined, some unexpected configurations have been found. Here, we describe a method to recover transgene insertion sites and assess structural rearrangements of host and transgene DNA using microarray hybridization and targeted sequence capture. We used information about the transgene insertion site to develop a polymerase chain reaction genotyping assay to distinguish heterozygous from homozygous transgenic animals. Although we worked with a bacterial artificial chromosome transgenic mouse line, this method can be used to analyse the integration site and configuration of any foreign DNA in a sequenced genome.
publisher	Oxford University Press
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616733/
_version_	1611967634695258112

Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene

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