Cargando…
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...
Autores principales: | , , , , , , , |
---|---|
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 |
_version_ | 1782181501388980224 |
---|---|
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. |
format | Text |
id | pubmed-2874680 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | S. Karger AG |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT thomasr agenomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT dukese agenomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT karlssonek agenomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT evansa agenomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT ellisp agenomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT lindbladtohk agenomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT langfordcf agenomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT breenm agenomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT thomasr genomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT dukese genomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT karlssonek genomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT evansa genomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT ellisp genomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT lindbladtohk genomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT langfordcf genomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis AT breenm genomeassemblyintegrateddog1mbbacmicroarrayacytogeneticresourceforcaninecancerstudiesandcomparativegenomicanalysis |