DNA copy number amplification profiling of human neoplasms

S. Myllykangas, J. Himberg, T. Böhling, B. Nagy, J. Hollmén, S. Knuutila

Research output: Contribution to journalArticle

81 Citations (Scopus)

Abstract

DNA copy number amplifications activate oncogenes and are hallmarks of nearly all advanced tumors. Amplified genes represent attractive targets for therapy, diagnostics and prognostics. To investigate DNA amplifications in different neoplasms, we performed a bibliomics survey using 838 published chromosomal comparative genomic hybridization studies and collected amplification data at chromosome band resolution from more than 4500 cases. Amplification profiles were determined for 73 distinct neoplasms. Neoplasms were clustered according to the amplification profiles, and frequently amplified chromosomal loci (amplification hot spots) were identified using computational modeling. To investigate the site specificity and mechanisms of gene amplifications, colocalization of amplification hot spots, cancer genes, fragile sites, virus integration sites and gene size cohorts were tested in a statistical framework. Amplification-based clustering demonstrated that cancers with similar etiology, cell-of-origin or topographical location have a tendency to obtain convergent amplification profiles. The identified amplification hot spots were colocalized with the known fragile sites, cancer genes and virus integration sites, but global statistical significance could not be ascertained. Large genes were significantly overrepresented on the fragile sites and the reported amplification hot spots. These findings indicate that amplifications are selected in the cancer tissue environment according to the qualitative traits and localization of cancer genes.

Original languageEnglish
Pages (from-to)7324-7332
Number of pages9
JournalOncogene
Volume25
Issue number55
DOIs
Publication statusPublished - Nov 23 2006

Fingerprint

Neoplasm Genes
DNA
Virus Integration
Neoplasms
Genes
Comparative Genomic Hybridization
Gene Amplification
Oncogenes
Cluster Analysis
Chromosomes
Therapeutics

Keywords

  • Bioinformatics
  • Cancer
  • Data mining
  • Fragile site
  • Gene amplification
  • Molecular pathology

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research
  • Genetics

Cite this

Myllykangas, S., Himberg, J., Böhling, T., Nagy, B., Hollmén, J., & Knuutila, S. (2006). DNA copy number amplification profiling of human neoplasms. Oncogene, 25(55), 7324-7332. https://doi.org/10.1038/sj.onc.1209717

DNA copy number amplification profiling of human neoplasms. / Myllykangas, S.; Himberg, J.; Böhling, T.; Nagy, B.; Hollmén, J.; Knuutila, S.

In: Oncogene, Vol. 25, No. 55, 23.11.2006, p. 7324-7332.

Research output: Contribution to journalArticle

Myllykangas, S, Himberg, J, Böhling, T, Nagy, B, Hollmén, J & Knuutila, S 2006, 'DNA copy number amplification profiling of human neoplasms', Oncogene, vol. 25, no. 55, pp. 7324-7332. https://doi.org/10.1038/sj.onc.1209717
Myllykangas S, Himberg J, Böhling T, Nagy B, Hollmén J, Knuutila S. DNA copy number amplification profiling of human neoplasms. Oncogene. 2006 Nov 23;25(55):7324-7332. https://doi.org/10.1038/sj.onc.1209717
Myllykangas, S. ; Himberg, J. ; Böhling, T. ; Nagy, B. ; Hollmén, J. ; Knuutila, S. / DNA copy number amplification profiling of human neoplasms. In: Oncogene. 2006 ; Vol. 25, No. 55. pp. 7324-7332.
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