Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays

Kevin K. Dobbin, David G. Beer, Matthew Meyerson, Timothy J. Yeatman, William L. Gerald, James W. Jacobson, Barbara Conley, Kenneth H. Buetow, Mervi Heiskanen, Richard M. Simon, John D. Minna, Luc Girard, David E. Misek, Jeremy M G Taylor, Samir Hanash, Katsuhiko Naoki, D. Neil Hayes, Christine Marie Ladd-Acosta, Steven A. Enkemann, Agnes VialeThomas J. Giordano

Research output: Contribution to journalArticle

Abstract

A key step in bringing gene expression data into clinical practice is the conduct of large studies to confirm preliminary models. The performance of such confirmatory studies and the transition to clinical practice requires that microarray data from different laboratories are comparable and reproducible. We designed a study to assess the comparability of data from four laboratories that will conduct a larger microarray profiling confirmation project in lung adenocarcinomas. To test the feasibility of combining data across laboratories, frozen tumor tissues, cell line pellets, and purified RNA samples were analyzed at each of the four laboratories. Samples of each type and several subsamples from each tumor and each cell line were blinded before being distributed. The laboratories followed a common protocol for all steps of tissue processing, RNA extraction, and microarray analysis using Affymetrix Human Genome U133A arrays. High within-laboratory and between-laboratory correlations were observed on the purified RNA samples, the cell lines, and the frozen tumor tissues. Intraclass correlation within laboratories was only slightly stronger than between laboratories, and the intraclass correlation tended to be weakest for genes expressed at low levels and showing small variation. Finally, hierarchical cluster analysis revealed that the repeated samples clustered together regardless of the laboratory in which the experiments were done. The findings indicate that under properly controlled conditions it is feasible to perform complete tumor microarray analysis, from tissue processing to hybridization and scanning, at multiple independent laboratories for a single study.

Original languageEnglish (US)
Pages (from-to)565-572
Number of pages8
JournalClinical Cancer Research
Volume11
Issue number2 I
StatePublished - Jan 15 2005
Externally publishedYes

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Neoplasm Genes
Oligonucleotide Array Sequence Analysis
Gene Expression
Tumor Cell Line
RNA
Tissue Array Analysis
Human Genome
Microarray Analysis
Cluster Analysis

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Dobbin, K. K., Beer, D. G., Meyerson, M., Yeatman, T. J., Gerald, W. L., Jacobson, J. W., ... Giordano, T. J. (2005). Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clinical Cancer Research, 11(2 I), 565-572.

Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. / Dobbin, Kevin K.; Beer, David G.; Meyerson, Matthew; Yeatman, Timothy J.; Gerald, William L.; Jacobson, James W.; Conley, Barbara; Buetow, Kenneth H.; Heiskanen, Mervi; Simon, Richard M.; Minna, John D.; Girard, Luc; Misek, David E.; Taylor, Jeremy M G; Hanash, Samir; Naoki, Katsuhiko; Hayes, D. Neil; Ladd-Acosta, Christine Marie; Enkemann, Steven A.; Viale, Agnes; Giordano, Thomas J.

In: Clinical Cancer Research, Vol. 11, No. 2 I, 15.01.2005, p. 565-572.

Research output: Contribution to journalArticle

Dobbin, KK, Beer, DG, Meyerson, M, Yeatman, TJ, Gerald, WL, Jacobson, JW, Conley, B, Buetow, KH, Heiskanen, M, Simon, RM, Minna, JD, Girard, L, Misek, DE, Taylor, JMG, Hanash, S, Naoki, K, Hayes, DN, Ladd-Acosta, CM, Enkemann, SA, Viale, A & Giordano, TJ 2005, 'Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays', Clinical Cancer Research, vol. 11, no. 2 I, pp. 565-572.
Dobbin KK, Beer DG, Meyerson M, Yeatman TJ, Gerald WL, Jacobson JW et al. Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clinical Cancer Research. 2005 Jan 15;11(2 I):565-572.
Dobbin, Kevin K. ; Beer, David G. ; Meyerson, Matthew ; Yeatman, Timothy J. ; Gerald, William L. ; Jacobson, James W. ; Conley, Barbara ; Buetow, Kenneth H. ; Heiskanen, Mervi ; Simon, Richard M. ; Minna, John D. ; Girard, Luc ; Misek, David E. ; Taylor, Jeremy M G ; Hanash, Samir ; Naoki, Katsuhiko ; Hayes, D. Neil ; Ladd-Acosta, Christine Marie ; Enkemann, Steven A. ; Viale, Agnes ; Giordano, Thomas J. / Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. In: Clinical Cancer Research. 2005 ; Vol. 11, No. 2 I. pp. 565-572.
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