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Novel tumor sampling strategies to enable microarray gene expression signatures in breast cancer: a study to determine feasibility and reproducibility in the context of clinical care.

Publication ,  Journal Article
Tebbit, CL; Zhai, J; Untch, BR; Ellis, MJ; Dressman, HK; Bentley, RC; Baker, JA; Marcom, PK; Nevins, JR; Marks, JR; Olson, JA
Published in: Breast Cancer Res Treat
December 2009

Feasibility and reproducibility of microarray biomarkers in clinical settings are doubted because of reliance on fresh frozen tissue. We sought to develop and validate a paradigm of frozen tissue collection from early breast tumors to enable use of microarray in oncology practice. Frozen core needle biopsies (CNBx) were collected from 150 clinical stage I patients during image-guided diagnostic biopsy and/or surgery. Histology and tumor content from frozen cores were compared to diagnostic specimens. Twenty-eight patients had microarray analysis to examine accuracy and reproducibility of predictive gene signatures developed for estrogen receptor (ER) and HER2. One hundred twenty-seven (85%) of 150 patients had at least one frozen core containing cancer suitable for microarray analysis. Larger tumor size, ex vivo biopsy, and use of a new specimen device increased the likelihood of obtaining adequate specimens. Sufficient quality RNA was obtained from 90% of tumor cores. Microarray signatures predicting ER and HER2 expression were developed in training sets of up to 363 surgical samples and were applied to microarray data obtained from core samples collected in clinical settings. In these samples, prediction of ER and HER2 expression achieved a sensitivity/specificity of 94%/100%, and 82%/72%, respectively. Predictions were reproducible in 83-100% of paired samples. Frozen CNBx can be readily obtained from most breast cancers without interfering with pathologic evaluation in routine clinical settings. Collection of tumor tissue at diagnostic biopsy and/or at surgery from lumpectomy specimens using image guidance resulted in sufficient samples for array analysis from over 90% of patients. Sampling of breast cancer for microarray data is reproducible and feasible in clinical practice and can yield signatures predictive of multiple breast cancer phenotypes.

Duke Scholars

Published In

Breast Cancer Res Treat

DOI

EISSN

1573-7217

Publication Date

December 2009

Volume

118

Issue

3

Start / End Page

635 / 643

Location

Netherlands

Related Subject Headings

  • Surgery, Computer-Assisted
  • Sensitivity and Specificity
  • Reproducibility of Results
  • Receptors, Estrogen
  • Receptor, erbB-2
  • Receptor, ErbB-2
  • Oncology & Carcinogenesis
  • Oligonucleotide Array Sequence Analysis
  • Neoplasm Staging
  • Humans
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Tebbit, C. L., Zhai, J., Untch, B. R., Ellis, M. J., Dressman, H. K., Bentley, R. C., … Olson, J. A. (2009). Novel tumor sampling strategies to enable microarray gene expression signatures in breast cancer: a study to determine feasibility and reproducibility in the context of clinical care. Breast Cancer Res Treat, 118(3), 635–643. https://doi.org/10.1007/s10549-008-0301-1
Tebbit, Christopher L., Jun Zhai, Brian R. Untch, Matthew J. Ellis, Holly K. Dressman, Rex C. Bentley, Jay A. Baker, et al. “Novel tumor sampling strategies to enable microarray gene expression signatures in breast cancer: a study to determine feasibility and reproducibility in the context of clinical care.Breast Cancer Res Treat 118, no. 3 (December 2009): 635–43. https://doi.org/10.1007/s10549-008-0301-1.
Tebbit CL, Zhai J, Untch BR, Ellis MJ, Dressman HK, Bentley RC, et al. Novel tumor sampling strategies to enable microarray gene expression signatures in breast cancer: a study to determine feasibility and reproducibility in the context of clinical care. Breast Cancer Res Treat. 2009 Dec;118(3):635–43.
Tebbit, Christopher L., et al. “Novel tumor sampling strategies to enable microarray gene expression signatures in breast cancer: a study to determine feasibility and reproducibility in the context of clinical care.Breast Cancer Res Treat, vol. 118, no. 3, Dec. 2009, pp. 635–43. Pubmed, doi:10.1007/s10549-008-0301-1.
Tebbit CL, Zhai J, Untch BR, Ellis MJ, Dressman HK, Bentley RC, Baker JA, Marcom PK, Nevins JR, Marks JR, Olson JA. Novel tumor sampling strategies to enable microarray gene expression signatures in breast cancer: a study to determine feasibility and reproducibility in the context of clinical care. Breast Cancer Res Treat. 2009 Dec;118(3):635–643.

Published In

Breast Cancer Res Treat

DOI

EISSN

1573-7217

Publication Date

December 2009

Volume

118

Issue

3

Start / End Page

635 / 643

Location

Netherlands

Related Subject Headings

  • Surgery, Computer-Assisted
  • Sensitivity and Specificity
  • Reproducibility of Results
  • Receptors, Estrogen
  • Receptor, erbB-2
  • Receptor, ErbB-2
  • Oncology & Carcinogenesis
  • Oligonucleotide Array Sequence Analysis
  • Neoplasm Staging
  • Humans