Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction

Gerald Quon, Syed Haider, Amit G. Deshwar, Ang Cui, Paul C. Boutros, Quaid Morris

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

Tumor heterogeneity is a limiting factor in cancer treatment and in the discovery of biomarkers to personalize it. We describe a computational purification tool, ISOpure, which directly addresses the effects of variable contamination by normal tissue in clinical tumor specimens. ISOpure uses a set of tumor expression profiles and a panel of healthy tissue expression profiles to generate a purified cancer profile for each tumor sample, and an estimate of the proportion of RNA originating from cancerous cells. Applying ISOpure before identifying gene signatures leads to significant improvements in the prediction of prognosis and other clinical variables in lung and prostate cancer.

Original languageEnglish (US)
Article number29
JournalGenome Medicine
Volume5
Issue number3
DOIs
StatePublished - Mar 28 2013
Externally publishedYes

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Transcriptome
Neoplasms
Lung Neoplasms
Prostatic Neoplasms
Biomarkers
RNA
Genes

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics
  • Molecular Biology
  • Molecular Medicine

Cite this

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. / Quon, Gerald; Haider, Syed; Deshwar, Amit G.; Cui, Ang; Boutros, Paul C.; Morris, Quaid.

In: Genome Medicine, Vol. 5, No. 3, 29, 28.03.2013.

Research output: Contribution to journalArticle

Quon, Gerald ; Haider, Syed ; Deshwar, Amit G. ; Cui, Ang ; Boutros, Paul C. ; Morris, Quaid. / Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. In: Genome Medicine. 2013 ; Vol. 5, No. 3.
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