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  • Oncogenomics
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Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors

Oncogene volume 26, pages 1499–1506 (2007)Cite this article

Abstract

A series of studies have been published that evaluate the chromosomal copy number changes of different tumor classes using array comparative genomic hybridization (array CGH); however, the chromosomal aberrations that distinguish the different tumor classes have not been fully characterized. Therefore, we performed a meta-analysis of different array CGH data sets in an attempt to classify samples tested across different platforms. As opposed to RNA expression, a common reference is used in dual channel CGH arrays: normal human DNA, theoretically facilitating cross-platform analysis. To this aim, cell line and primary cancer data sets from three different dual channel array CGH platforms obtained by four different institutes were integrated. The cell line data were used to develop preprocessing methods, which performed noise reduction and transformed samples into a common format. The transformed array CGH profiles allowed perfect clustering by cell line, but importantly not by platform or institute. The same preprocessing procedures used for the cell line data were applied to data from 373 primary tumors profiled by array CGH, including controls. Results indicated that there is no apparent feature related to the institute or platform and that array CGH allows for unambiguous cross-platform meta-analysis. Major clusters with common tissue origin were identified. Interestingly, tumors of hematopoietic and mesenchymal origins cluster separately from tumors of epithelial origin. Therefore, it can be concluded that chromosomal aberrations of tumors from hematopoietic and mesenchymal origin versus tumors of epithelial origin are distinct, and these differences can be picked up by meta-analysis of array CGH data. This suggests the possibility of prospectively using combined analysis of diverse copy number data sets for cancer subtype classification.

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Acknowledgements

We thank Tony Cox, Ian Stalker (Sanger Institute, UK) and Nir Gamliel (Compugen USA, San Jose, CA, USA) for mapping the oligos into ENSEMBL. In addition, we would like to thank Cindy Postma and Erik Hopmans for their help with array hybridizations. We wish to thank Dr Stephen Ethier for the SUM cell lines and Dr Morag McCallum for the VP cell lines. SFC and CC are funded by Cancer Research UK. SFC was furthermore funded by COST-STSM B19. We furthermore acknowledge funding by the EU-sixth framework project: DISMAL, Contract No.: LSHC-CT-2005-018911. The work on the primary colon tumors at VUMC was supported by the Dutch Cancer Society Grant KWF-VU 02-2618.

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Authors and Affiliations

  1. Faculty of Sciences, Vrije Universiteit (VU), Amsterdam, The Netherlands

    K Jong, E Marchiori & A van der Vaart

  2. Department of Oncology, Cancer Genomics Program, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK

    S-F Chin & C Caldas

  3. Department of Pathology, Micro Array Core Facility, VU University Medical Center (VUMC), Amsterdam, The Netherlands

    B Carvalho, M Tijssen, P P Eijk, P van den IJssel, J J Oudejans, G A Meijer & B Ylstra

  4. Department of Pathology and Tumour Biology, St James's University Hospital, Leeds, UK

    H Grabsch & P Quirke

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  1. K Jong
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  12. G A Meijer
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Correspondence to B Ylstra.

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Supplementary Information accompanies the paper on the Oncogene website (http://www.nature.com/onc).

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Jong, K., Marchiori, E., van der Vaart, A. et al. Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors. Oncogene 26, 1499–1506 (2007). https://doi.org/10.1038/sj.onc.1209919

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