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A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis

Molecular cytogenetic studies have been instrumental in defining the nature of numerical and structural chromosome changes in human cancers, but their significance remains to be fully understood. The emergence of high quality genome assemblies for several model organisms provides exciting opportunit...

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Autores principales: Thomas, R., Duke, S.E., Karlsson, E.K., Evans, A., Ellis, P., Lindblad-Toh, K., Langford, C.F., Breen, M.
Formato: Texto
Lenguaje:English
Publicado: S. Karger AG 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874680/
https://www.ncbi.nlm.nih.gov/pubmed/19096206
http://dx.doi.org/10.1159/000163088
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author Thomas, R.
Duke, S.E.
Karlsson, E.K.
Evans, A.
Ellis, P.
Lindblad-Toh, K.
Langford, C.F.
Breen, M.
author_facet Thomas, R.
Duke, S.E.
Karlsson, E.K.
Evans, A.
Ellis, P.
Lindblad-Toh, K.
Langford, C.F.
Breen, M.
author_sort Thomas, R.
collection PubMed
description Molecular cytogenetic studies have been instrumental in defining the nature of numerical and structural chromosome changes in human cancers, but their significance remains to be fully understood. The emergence of high quality genome assemblies for several model organisms provides exciting opportunities to develop novel genome-integrated molecular cytogenetic resources that now permit a comparative approach to evaluating the relevance of tumor-associated chromosome aberrations, both within and between species. We have used the dog genome sequence assembly to identify a framework panel of 2,097 bacterial artificial chromosome (BAC) clones, selected at intervals of approximately one megabase. Each clone has been evaluated by multicolor fluorescence in situ hybridization (FISH) to confirm its unique cytogenetic location in concordance with its reported position in the genome assembly, providing new information on the organization of the dog genome. This panel of BAC clones also represents a powerful cytogenetic resource with numerous potential applications. We have used the clone set to develop a genome-wide microarray for comparative genomic hybridization (aCGH) analysis, and demonstrate its application in detection of tumor-associated DNA copy number aberrations (CNAs) including single copy deletions and amplifications, regional aneuploidy and whole chromosome aneuploidy. We also show how individual clones selected from the BAC panel can be used as FISH probes in direct evaluation of tumor karyotypes, to verify and explore CNAs detected using aCGH analysis. This cytogenetically validated, genome integrated BAC clone panel has enormous potential for aiding gene discovery through a comparative approach to molecular oncology.
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spelling pubmed-28746802010-06-08 A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis Thomas, R. Duke, S.E. Karlsson, E.K. Evans, A. Ellis, P. Lindblad-Toh, K. Langford, C.F. Breen, M. Cytogenet Genome Res Original Article Molecular cytogenetic studies have been instrumental in defining the nature of numerical and structural chromosome changes in human cancers, but their significance remains to be fully understood. The emergence of high quality genome assemblies for several model organisms provides exciting opportunities to develop novel genome-integrated molecular cytogenetic resources that now permit a comparative approach to evaluating the relevance of tumor-associated chromosome aberrations, both within and between species. We have used the dog genome sequence assembly to identify a framework panel of 2,097 bacterial artificial chromosome (BAC) clones, selected at intervals of approximately one megabase. Each clone has been evaluated by multicolor fluorescence in situ hybridization (FISH) to confirm its unique cytogenetic location in concordance with its reported position in the genome assembly, providing new information on the organization of the dog genome. This panel of BAC clones also represents a powerful cytogenetic resource with numerous potential applications. We have used the clone set to develop a genome-wide microarray for comparative genomic hybridization (aCGH) analysis, and demonstrate its application in detection of tumor-associated DNA copy number aberrations (CNAs) including single copy deletions and amplifications, regional aneuploidy and whole chromosome aneuploidy. We also show how individual clones selected from the BAC panel can be used as FISH probes in direct evaluation of tumor karyotypes, to verify and explore CNAs detected using aCGH analysis. This cytogenetically validated, genome integrated BAC clone panel has enormous potential for aiding gene discovery through a comparative approach to molecular oncology. S. Karger AG 2008-12 /pmc/articles/PMC2874680/ /pubmed/19096206 http://dx.doi.org/10.1159/000163088 Text en Copyright © 2008 by S. Karger AG, Basel http://creativecommons.org/licenses/by-nc/3.0/ This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License (http://creativecommons.org/licenses/by-nc/3.0/). Users may download, print and share this work on the Internet for noncommercial purposes only, provided the original work is properly cited, and a link to the original work on http://www.karger.com as well as the terms of this license are included in any shared versions.
spellingShingle Original Article
Thomas, R.
Duke, S.E.
Karlsson, E.K.
Evans, A.
Ellis, P.
Lindblad-Toh, K.
Langford, C.F.
Breen, M.
A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis
title A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis
title_full A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis
title_fullStr A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis
title_full_unstemmed A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis
title_short A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis
title_sort genome assembly-integrated dog 1 mb bac microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874680/
https://www.ncbi.nlm.nih.gov/pubmed/19096206
http://dx.doi.org/10.1159/000163088
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