An integrated study of aberrant gene copy number and gene expression in GIST and LMS

Da Yang, Antti Ylipää, Jilong Yang, Kelly Hunt, Raphael Pollock, Jonathan Trent, Olli Yli-Harja, Ilya Shmulevich, Matti Nykter, Wei Zhang

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Increased chromosomal instability that alters the gene copy numbers throughout the genome is known to have a role in molecular pathogenesis of tumors. The impact of gene dosage effect to the expression levels of genes in GIST and LMS is unknown. In this paper, we used a combination of array comparative genomic hybridization (aCGH) and gene expression data to gain insights into the interplay of structural and functional changes of the genome in GIST and LMSs. We identified specific target genes that change their expression due to the gene dosage effect. Statistical analysis identified four chromosomal regions, 1p, 14q, 15q, and 22q, where both copy number and mRNA expression were significantly different between the tumor types. Multi-dimensional scaling (MDS) analysis showed that the gene expression profiles of these four regions accurately distinguish GIST and LMS. In addition, the gene dosage sensitive genes in these regions are differently involved in several tumor growth promoting pathways, implying that there are different mechanisms underlying the GIST and LMS carcinogenesis. Integration of aCGH and gene expression data has not only provided insights into how DNA copy number variations affect the gene expression patterns in these cancers, but also proves to be a promising method to choose biologically relevant biomarkers.

Original languageEnglish
Pages (from-to)171-177
Number of pages7
JournalTechnology in Cancer Research and Treatment
Volume9
Issue number2
StatePublished - Apr 1 2010
Externally publishedYes

Fingerprint

Gene Dosage
Gene Expression
Comparative Genomic Hybridization
Neoplasms
DNA Copy Number Variations
Genome
Chromosomal Instability
Transcriptome
Genes
Carcinogenesis
Biomarkers
Messenger RNA
Growth

Keywords

  • Array CGH
  • CNA
  • Gene expression
  • GIST
  • Leiomyosarcoma

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Yang, D., Ylipää, A., Yang, J., Hunt, K., Pollock, R., Trent, J., ... Zhang, W. (2010). An integrated study of aberrant gene copy number and gene expression in GIST and LMS. Technology in Cancer Research and Treatment, 9(2), 171-177.

An integrated study of aberrant gene copy number and gene expression in GIST and LMS. / Yang, Da; Ylipää, Antti; Yang, Jilong; Hunt, Kelly; Pollock, Raphael; Trent, Jonathan; Yli-Harja, Olli; Shmulevich, Ilya; Nykter, Matti; Zhang, Wei.

In: Technology in Cancer Research and Treatment, Vol. 9, No. 2, 01.04.2010, p. 171-177.

Research output: Contribution to journalArticle

Yang, D, Ylipää, A, Yang, J, Hunt, K, Pollock, R, Trent, J, Yli-Harja, O, Shmulevich, I, Nykter, M & Zhang, W 2010, 'An integrated study of aberrant gene copy number and gene expression in GIST and LMS', Technology in Cancer Research and Treatment, vol. 9, no. 2, pp. 171-177.
Yang D, Ylipää A, Yang J, Hunt K, Pollock R, Trent J et al. An integrated study of aberrant gene copy number and gene expression in GIST and LMS. Technology in Cancer Research and Treatment. 2010 Apr 1;9(2):171-177.
Yang, Da ; Ylipää, Antti ; Yang, Jilong ; Hunt, Kelly ; Pollock, Raphael ; Trent, Jonathan ; Yli-Harja, Olli ; Shmulevich, Ilya ; Nykter, Matti ; Zhang, Wei. / An integrated study of aberrant gene copy number and gene expression in GIST and LMS. In: Technology in Cancer Research and Treatment. 2010 ; Vol. 9, No. 2. pp. 171-177.
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