TNBCtype: A subtyping tool for triple-negative breast cancer

Xi Chen, Jiang Li, William H. Gray, Brian D. Lehmann, Joshua A. Bauer, Yu Shyr, Jennifer A. Pietenpol

Research output: Contribution to journalArticle

105 Citations (Scopus)

Abstract

Motivation: Triple-negative breast cancer (TNBC) is a heterogeneous breast cancer group, and identification of molecular subtypes is essential for understanding the biological characteristics and clinical behaviors of TNBC as well as for developing personalized treatments. Based on 3,247 gene expression profiles from 21 breast cancer data sets, we discovered six TNBC subtypes from 587 TNBC samples with unique gene expression patterns and ontologies. Cell line models representing each of the TNBC subtypes also displayed different sensitivities to targeted therapeutic agents. Classification of TNBC into subtypes will advance further genomic research and clinical applications. Result: We developed a web-based subtyping tool TNBCtype for candidate TNBC samples using our gene expression meta data and classification methods. Given a gene expression data matrix, this tool will display for each candidate sample the predicted subtype, the corresponding correlation coefficient, and the permutation P-value. We offer a user-friendly web interface to predict the subtypes for new TNBC samples that may facilitate diagnostics, biomarker selection, drug discovery, and the more tailored treatment of breast cancer.

Original languageEnglish (US)
Pages (from-to)147-156
Number of pages10
JournalCancer Informatics
Volume11
DOIs
StatePublished - Aug 10 2012
Externally publishedYes

Fingerprint

Triple Negative Breast Neoplasms
Breast Neoplasms
Gene Expression
Social Identification
Gene Ontology
Drug Discovery
Transcriptome
Biomarkers
Cell Line

Keywords

  • Classification
  • Gene expression microarray
  • Meta-analysis
  • Subtypes
  • Triple-negative breast cancer

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Chen, X., Li, J., Gray, W. H., Lehmann, B. D., Bauer, J. A., Shyr, Y., & Pietenpol, J. A. (2012). TNBCtype: A subtyping tool for triple-negative breast cancer. Cancer Informatics, 11, 147-156. https://doi.org/10.4137/CIN.S9983

TNBCtype : A subtyping tool for triple-negative breast cancer. / Chen, Xi; Li, Jiang; Gray, William H.; Lehmann, Brian D.; Bauer, Joshua A.; Shyr, Yu; Pietenpol, Jennifer A.

In: Cancer Informatics, Vol. 11, 10.08.2012, p. 147-156.

Research output: Contribution to journalArticle

Chen, X, Li, J, Gray, WH, Lehmann, BD, Bauer, JA, Shyr, Y & Pietenpol, JA 2012, 'TNBCtype: A subtyping tool for triple-negative breast cancer', Cancer Informatics, vol. 11, pp. 147-156. https://doi.org/10.4137/CIN.S9983
Chen X, Li J, Gray WH, Lehmann BD, Bauer JA, Shyr Y et al. TNBCtype: A subtyping tool for triple-negative breast cancer. Cancer Informatics. 2012 Aug 10;11:147-156. https://doi.org/10.4137/CIN.S9983
Chen, Xi ; Li, Jiang ; Gray, William H. ; Lehmann, Brian D. ; Bauer, Joshua A. ; Shyr, Yu ; Pietenpol, Jennifer A. / TNBCtype : A subtyping tool for triple-negative breast cancer. In: Cancer Informatics. 2012 ; Vol. 11. pp. 147-156.
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