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Array CGH demonstrates characteristic aberration signatures in human papillary thyroid carcinomas governed by RET/PTC

Abstract

The aim of this study is to investigate additional genetic alterations in papillary thyroid carcinomas (PTCs) with known RET/PTC rearrangements. We applied array-based comparative genomic hybridization (array CGH) to 33 PTC (20 PTC from adults, 13 post-Chernobyl PTC from children) with known RET/PTC status. Principal component analysis and hierarchical cluster analysis identified cases with similar aberration patterns. Significant deviations between tumour-groups were obtained by statistical testing (Fisher's exact test in combination with Benjamini–Hochberg FDR-controlling procedure). FISH analysis on FFPE sections was applied to validate the array CGH data. Deletions were found more frequently in RET/PTC-positive and RET/PTC-negative tumours than amplifications. Specific aberration signatures were identified that discriminated between RET/PTC-positive and RET/PTC-negative cases (aberrations on chromosomes 1p, 3q, 4p, 7p, 9p/q, 10q, 12q, 13q and 21q). In addition, childhood and adult RET/PTC-positive cases differ significantly for a deletion on the distal part of chromosome 1p. There are additional alterations in RET/PTC-positive tumours, which may act as modifiers of RET activation. In contrast, alterations in RET/PTC-negative tumours indicate alternative routes of tumour development. The data presented serve as a starting point for further studies on gene expression and function of genes identified in this study.

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Abbreviations

BAC:

bacterial artificial chromosome

CGH:

comparative genomic hybridization

FISH:

fluorescence in situ hybridization

PTC:

papillary thyroid carcinoma

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Acknowledgements

We acknowledge Elke Konhäuser for the skilful technical assistance and Cordelia Langford and the Wellcome Trust Sanger Institute microarray facility for supplying the 1-Mb BAC arrays. This study was supported in part by EC Grant FP6-36495 and a grant from the German Cancer Aid (project no. 108033).

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Correspondence to H Zitzelsberger.

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

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Unger, K., Malisch, E., Thomas, G. et al. Array CGH demonstrates characteristic aberration signatures in human papillary thyroid carcinomas governed by RET/PTC. Oncogene 27, 4592–4602 (2008). https://doi.org/10.1038/onc.2008.99

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