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Interlaboratory Comparability Study of Cancer Gene Expression Analysis Using Oligonucleotide Microarrays

¹ Cancer Diagnosis Program, ² Biometric Research Branch, and ³ Center for Bioinformatics, National Cancer Institute, Bethesda, Maryland; Departments of ⁴ Surgery, ⁵ Pediatrics, and ⁶ Pathology, University of Michigan Medical School and ⁷ Department of Biostatistics, University of Michigan, Ann Arbor, Michigan; ⁸ Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Pathology, Harvard Medical School, Boston, Massachusetts; ⁹ Department of Surgery, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, Florida; Departments of ¹⁰ Pathology and ¹¹ Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, New York; ¹² Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas; and ¹³ Whitehead Institute-Massachusetts Institute of Technology Center for Genome Research, Cambridge, Massachusetts

Requests for reprints: Kevin K. Dobbin, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD 20852. Phone: 301-451-6244; E-mail: dobbinke{at}mail.nih.gov.

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.

Key Words: oligonucleotide microarrays • reproducibility • interlaboratory comparison • gene expression

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