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

Nicolas Wicker, Annaïck Carles, Ian G. Mills, Maija Wolf, Abhi Veerakumarasivam, Henrik Edgren, Fabrice Boileau, Bohdan Wasylyk, Jack A. Schalken, David E. Neal, Olli Kallioniemi, Olivier Poch

Research output: Contribution to journalArticleScientificpeer-review

31 Citations (Scopus)

Abstract

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. Conclusions 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.
Original languageEnglish
Number of pages10
JournalBMC Genomics
Volume8
Issue number84
DOIs
Publication statusPublished - 2007
MoE publication typeA1 Journal article-refereed

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Bacterial Artificial Chromosomes
Comparative Genomic Hybridization
Statistical Models
Technology
DNA
Oligonucleotides
Prostatic Neoplasms
Genome

Cite this

Wicker, N., Carles, A., Mills, I. G., Wolf, M., Veerakumarasivam, A., Edgren, H., ... Poch, O. (2007). A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. BMC Genomics, 8(84). https://doi.org/10.1186/1471-2164-8-84
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. In: BMC Genomics. 2007 ; Vol. 8, No. 84.
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abstract = "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. Conclusions 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.",
author = "Nicolas Wicker and Anna{\"i}ck Carles and Mills, {Ian G.} and Maija Wolf and Abhi Veerakumarasivam and Henrik Edgren and Fabrice Boileau and Bohdan Wasylyk and Schalken, {Jack A.} and Neal, {David E.} and Olli Kallioniemi and Olivier Poch",
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Wicker, N, Carles, A, Mills, IG, Wolf, M, Veerakumarasivam, A, Edgren, H, Boileau, F, Wasylyk, B, Schalken, JA, Neal, DE, Kallioniemi, O & Poch, O 2007, 'A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH', BMC Genomics, vol. 8, no. 84. https://doi.org/10.1186/1471-2164-8-84

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.

In: BMC Genomics, Vol. 8, No. 84, 2007.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH

AU - Wicker, Nicolas

AU - Carles, Annaïck

AU - Mills, Ian G.

AU - Wolf, Maija

AU - Veerakumarasivam, Abhi

AU - Edgren, Henrik

AU - Boileau, Fabrice

AU - Wasylyk, Bohdan

AU - Schalken, Jack A.

AU - Neal, David E.

AU - Kallioniemi, Olli

AU - Poch, Olivier

PY - 2007

Y1 - 2007

N2 - 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. Conclusions 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.

AB - 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. Conclusions 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.

U2 - 10.1186/1471-2164-8-84

DO - 10.1186/1471-2164-8-84

M3 - Article

VL - 8

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 84

ER -