A methodology for utilization of predictive genomic signatures in FFPE samples

Jennifer A. Freedman, Christina K. Augustine, Angelica M. Selim, Kirsten C. Holshausen, Zhengzheng Wei, Katherine A. Tsamis, David S. Hsu, Holly K. Dressman, William T. Barry, Douglas Tyler, Joseph R. Nevins

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: Gene expression signatures developed to measure the activity of oncogenic signaling pathways have been used to dissect the heterogeneity of tumor samples and to predict sensitivity to various cancer drugs that target components of the relevant pathways, thus potentially identifying therapeutic options for subgroups of patients. To facilitate broad use, including in a clinical setting, the ability to generate data from formalin-fixed, paraffin-embedded (FFPE) tissues is essential. Methods. Patterns of pathway activity in matched fresh-frozen and FFPE xenograft tumor samples were generated using the MessageAmp Premier methodology in combination with assays using Affymetrix arrays. Results generated were compared with those obtained from fresh-frozen samples using a standard Affymetrix assay. In addition, gene expression data from patient matched fresh-frozen and FFPE melanomas were also utilized to evaluate the consistency of predictions of oncogenic signaling pathway status. Results: Significant correlation was observed between pathway activity predictions from paired fresh-frozen and FFPE xenograft tumor samples. In addition, significant concordance of pathway activity predictions was also observed between patient matched fresh-frozen and FFPE melanomas. Conclusions: Reliable and consistent predictions of oncogenic pathway activities can be obtained from FFPE tumor tissue samples. The ability to reliably utilize FFPE patient tumor tissue samples for genomic analyses will lead to a better understanding of the biology of disease progression and, in the clinical setting, will provide tools to guide the choice of therapeutics to those most likely to be effective in treating a patient's disease.

Original languageEnglish (US)
Article number58
JournalBMC Medical Genomics
Volume4
DOIs
StatePublished - 2011
Externally publishedYes

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Paraffin
Formaldehyde
Neoplasms
Heterografts
Melanoma
Transcriptome
Disease Progression
Gene Expression
Therapeutics
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

Freedman, J. A., Augustine, C. K., Selim, A. M., Holshausen, K. C., Wei, Z., Tsamis, K. A., ... Nevins, J. R. (2011). A methodology for utilization of predictive genomic signatures in FFPE samples. BMC Medical Genomics, 4, [58]. https://doi.org/10.1186/1755-8794-4-58

A methodology for utilization of predictive genomic signatures in FFPE samples. / Freedman, Jennifer A.; Augustine, Christina K.; Selim, Angelica M.; Holshausen, Kirsten C.; Wei, Zhengzheng; Tsamis, Katherine A.; Hsu, David S.; Dressman, Holly K.; Barry, William T.; Tyler, Douglas; Nevins, Joseph R.

In: BMC Medical Genomics, Vol. 4, 58, 2011.

Research output: Contribution to journalArticle

Freedman, JA, Augustine, CK, Selim, AM, Holshausen, KC, Wei, Z, Tsamis, KA, Hsu, DS, Dressman, HK, Barry, WT, Tyler, D & Nevins, JR 2011, 'A methodology for utilization of predictive genomic signatures in FFPE samples', BMC Medical Genomics, vol. 4, 58. https://doi.org/10.1186/1755-8794-4-58
Freedman JA, Augustine CK, Selim AM, Holshausen KC, Wei Z, Tsamis KA et al. A methodology for utilization of predictive genomic signatures in FFPE samples. BMC Medical Genomics. 2011;4. 58. https://doi.org/10.1186/1755-8794-4-58
Freedman, Jennifer A. ; Augustine, Christina K. ; Selim, Angelica M. ; Holshausen, Kirsten C. ; Wei, Zhengzheng ; Tsamis, Katherine A. ; Hsu, David S. ; Dressman, Holly K. ; Barry, William T. ; Tyler, Douglas ; Nevins, Joseph R. / A methodology for utilization of predictive genomic signatures in FFPE samples. In: BMC Medical Genomics. 2011 ; Vol. 4.
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