Evaluating translocation gene fusions by SNP array data

Hong Liu, Asher Zilberstein, Pascal Pannier, Frederic Fleche, Christopher Arendt, Christoph Lengauer, Chang S. Hahn

Research output: Contribution to journalArticle

Abstract

Somatic cell genetic alterations are a hallmark of tumor development and progression. Although various technologies have been developed and utilized to identify genetic aberrations, identifying genetic translocations at the chromosomal level is still a challenging task. High density SNP microarrays are useful to measure DNA copy number variation (CNV) across the genome. Utilizing SNP array data of cancer cell lines and patient samples, we evaluated the CNV and copy number breakpoints for several known fusion genes implicated in tumorigenesis. This analysis demonstrated the potential utility of SNP array data for the prediction of genetic aberrations via translocations based on identifying copy number breakpoints within the target genes. Genome-wide analysis was also performed to identify genes harboring copy number breakpoints across 820 cancer cell lines. Candidate oncogenes were identified that are linked to potential translocations in specific cancer cell lines.

Original languageEnglish (US)
Pages (from-to)15-27
Number of pages13
JournalCancer Informatics
Volume11
DOIs
StatePublished - 2012
Externally publishedYes

Fingerprint

Gene Fusion
Single Nucleotide Polymorphism
Cell Line
Neoplasms
DNA Copy Number Variations
Genome
Genetic Translocation
Gene Dosage
Oncogenes
Carcinogenesis
Technology
Genes

Keywords

  • Copy number breakpoint
  • Copy number variation
  • SNP array
  • Translocation

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Liu, H., Zilberstein, A., Pannier, P., Fleche, F., Arendt, C., Lengauer, C., & Hahn, C. S. (2012). Evaluating translocation gene fusions by SNP array data. Cancer Informatics, 11, 15-27. https://doi.org/10.4137/CIN.S8026

Evaluating translocation gene fusions by SNP array data. / Liu, Hong; Zilberstein, Asher; Pannier, Pascal; Fleche, Frederic; Arendt, Christopher; Lengauer, Christoph; Hahn, Chang S.

In: Cancer Informatics, Vol. 11, 2012, p. 15-27.

Research output: Contribution to journalArticle

Liu, H, Zilberstein, A, Pannier, P, Fleche, F, Arendt, C, Lengauer, C & Hahn, CS 2012, 'Evaluating translocation gene fusions by SNP array data', Cancer Informatics, vol. 11, pp. 15-27. https://doi.org/10.4137/CIN.S8026
Liu H, Zilberstein A, Pannier P, Fleche F, Arendt C, Lengauer C et al. Evaluating translocation gene fusions by SNP array data. Cancer Informatics. 2012;11:15-27. https://doi.org/10.4137/CIN.S8026
Liu, Hong ; Zilberstein, Asher ; Pannier, Pascal ; Fleche, Frederic ; Arendt, Christopher ; Lengauer, Christoph ; Hahn, Chang S. / Evaluating translocation gene fusions by SNP array data. In: Cancer Informatics. 2012 ; Vol. 11. pp. 15-27.
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