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Small regions of overlapping deletions on 6q26 in human astrocytic tumours identified using chromosome 6 tile path array-CGH

Oncogene volume 25, pages 1261–1271 (2006)Cite this article

Abstract

Deletions of chromosome 6 are a common abnormality in diverse human malignancies including astrocytic tumours, suggesting the presence of tumour suppressor genes (TSG). In order to help identify candidate TSGs, we have constructed a chromosome 6 tile path microarray. The array contains 1780 clones (778 P1-derived artificial chromosome and 1002 bacterial artificial chromosome) that cover 98.3% of the published chromosome 6 sequences. A total of 104 adult astrocytic tumours (10 diffuse astrocytomas, 30 anaplastic astrocytomas (AA), 64 glioblastomas (GB)) were analysed using this array. Single copy number change was successfully detected and the result was in general concordant with a microsatellite analysis. The pattern of copy number change was complex with multiple interstitial deletions/gains. However, a predominance of telomeric 6q deletions was seen. Two small common and overlapping regions of deletion at 6q26 were identified. One was 1002?kb in size and contained PACRG and QKI, while the second was 199?kb and harbours a single gene, ARID1B. The data show that the chromosome 6 tile path array is useful in mapping copy number changes with high resolution and accuracy. We confirmed the high frequency of chromosome 6 deletions in AA and GB, and identified two novel commonly deleted regions that may harbour TSGs.

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Abbreviations

CGH:

comparative genomic hybridization

TSG:

tumour suppressor gene

MSA:

microsatellite analysis

PAC:

P1-derived artificial chromosome

BAC:

bacterial artificial chromosome

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Acknowledgements

We thank the Mapping Core, Map Finishing and Microarray Facility groups of the Wellcome Trust Sanger Institute, Hinxton, UK, for initial clone supply and verification, the Centre for Microarray resources in the Department of Pathology, University of Cambridge, for printing of the arrays, and David A Carter for excellent technical assistance. This work was supported by grants from Cancer Research UK, The Jacqueline Seroussi Memorial Foundation for Cancer Research, Samantha Dickson Research Trust, CAMPOD, the Ludwig Institute for Cancer Research and the Wellcome Trust.

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Authors and Affiliations

  1. Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK

    K Ichimura, D M Pearson & V Peter Collins

  2. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

    A J Mungall, H Fiegler, I Dunham & N P Carter

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  1. K Ichimura
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  2. A J Mungall
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  3. H Fiegler
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  7. V Peter Collins
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Correspondence to K Ichimura.

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

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Ichimura, K., Mungall, A., Fiegler, H. et al. Small regions of overlapping deletions on 6q26 in human astrocytic tumours identified using chromosome 6 tile path array-CGH. Oncogene 25, 1261–1271 (2006). https://doi.org/10.1038/sj.onc.1209156

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