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A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH

BACKGROUND: Currently, two main technologies are used for screening of DNA copy number; the BAC (Bacterial Artificial Chromosome) and the recently developed oligonucleotide-based CGH (Chromosomal Comparative Genomic Hybridization) arrays which are capable of detecting small genomic regions with ampl...

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Autores principales: Wicker, Nicolas, Carles, Annaïck, Mills, Ian G, Wolf, Maija, Veerakumarasivam, Abhi, Edgren, Henrik, Boileau, Fabrice, Wasylyk, Bohdan, Schalken, Jack A, Neal, David E, Kallioniemi, Olli, Poch, Olivier
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852311/
https://www.ncbi.nlm.nih.gov/pubmed/17394638
http://dx.doi.org/10.1186/1471-2164-8-84
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author Wicker, Nicolas
Carles, Annaïck
Mills, Ian G
Wolf, Maija
Veerakumarasivam, Abhi
Edgren, Henrik
Boileau, Fabrice
Wasylyk, Bohdan
Schalken, Jack A
Neal, David E
Kallioniemi, Olli
Poch, Olivier
author_facet Wicker, Nicolas
Carles, Annaïck
Mills, Ian G
Wolf, Maija
Veerakumarasivam, Abhi
Edgren, Henrik
Boileau, Fabrice
Wasylyk, Bohdan
Schalken, Jack A
Neal, David E
Kallioniemi, Olli
Poch, Olivier
author_sort Wicker, Nicolas
collection PubMed
description BACKGROUND: Currently, two main technologies are used for screening of DNA copy number; the BAC (Bacterial Artificial Chromosome) and the recently developed oligonucleotide-based CGH (Chromosomal Comparative Genomic Hybridization) arrays which are capable of detecting small genomic regions with amplification or deletion. The correlation as well as the discriminative power of these platforms has never been compared statistically on a significant set of human patient samples. RESULTS: In this paper, we present an exhaustive comparison between the two CGH platforms, undertaken at two independent sites using the same batch of DNA from 19 advanced prostate cancers. The comparison was performed directly on the raw data and a significant correlation was found between the two platforms. The correlation was greatly improved when the data were averaged over large chromosomic regions using a segmentation algorithm. In addition, this analysis has enabled the development of a statistical model to discriminate BAC outliers that might indicate microevents. These microevents were validated by the oligo platform results. CONCLUSION: This article presents a genome-wide statistical validation of the oligo array platform on a large set of patient samples and demonstrates statistically its superiority over the BAC platform for the Identification of chromosomic events. Taking advantage of a large set of human samples treated by the two technologies, a statistical model has been developed to show that the BAC platform could also detect microevents.
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spelling pubmed-18523112007-04-17 A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH Wicker, Nicolas Carles, Annaïck Mills, Ian G Wolf, Maija Veerakumarasivam, Abhi Edgren, Henrik Boileau, Fabrice Wasylyk, Bohdan Schalken, Jack A Neal, David E Kallioniemi, Olli Poch, Olivier BMC Genomics Methodology Article BACKGROUND: Currently, two main technologies are used for screening of DNA copy number; the BAC (Bacterial Artificial Chromosome) and the recently developed oligonucleotide-based CGH (Chromosomal Comparative Genomic Hybridization) arrays which are capable of detecting small genomic regions with amplification or deletion. The correlation as well as the discriminative power of these platforms has never been compared statistically on a significant set of human patient samples. RESULTS: In this paper, we present an exhaustive comparison between the two CGH platforms, undertaken at two independent sites using the same batch of DNA from 19 advanced prostate cancers. The comparison was performed directly on the raw data and a significant correlation was found between the two platforms. The correlation was greatly improved when the data were averaged over large chromosomic regions using a segmentation algorithm. In addition, this analysis has enabled the development of a statistical model to discriminate BAC outliers that might indicate microevents. These microevents were validated by the oligo platform results. CONCLUSION: This article presents a genome-wide statistical validation of the oligo array platform on a large set of patient samples and demonstrates statistically its superiority over the BAC platform for the Identification of chromosomic events. Taking advantage of a large set of human samples treated by the two technologies, a statistical model has been developed to show that the BAC platform could also detect microevents. BioMed Central 2007-03-29 /pmc/articles/PMC1852311/ /pubmed/17394638 http://dx.doi.org/10.1186/1471-2164-8-84 Text en Copyright © 2007 Wicker et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Wicker, Nicolas
Carles, Annaïck
Mills, Ian G
Wolf, Maija
Veerakumarasivam, Abhi
Edgren, Henrik
Boileau, Fabrice
Wasylyk, Bohdan
Schalken, Jack A
Neal, David E
Kallioniemi, Olli
Poch, Olivier
A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH
title A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH
title_full A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH
title_fullStr A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH
title_full_unstemmed A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH
title_short A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH
title_sort new look towards bac-based array cgh through a comprehensive comparison with oligo-based array cgh
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852311/
https://www.ncbi.nlm.nih.gov/pubmed/17394638
http://dx.doi.org/10.1186/1471-2164-8-84
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