title: Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays.
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.
authors.affiliation: Cancer Diagnosis Program, National Cancer Institute/NIH, Bethesda, MD 20894, USA. dobbinke@mail.nih.gov
authors.forename: Kevin K
authors.initials: KK
authors.lastname: Dobbin
authors.forename: David G
authors.initials: DG
authors.lastname: Beer
authors.forename: Matthew
authors.initials: M
authors.lastname: Meyerson
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Yeatman
authors.forename: William L
authors.initials: WL
authors.lastname: Gerald
authors.forename: James W
authors.initials: JW
authors.lastname: Jacobson
authors.forename: Barbara
authors.initials: B
authors.lastname: Conley
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Buetow
authors.forename: Mervi
authors.initials: M
authors.lastname: Heiskanen
authors.forename: Richard M
authors.initials: RM
authors.lastname: Simon
authors.forename: John D
authors.initials: JD
authors.lastname: Minna
authors.forename: Luc
authors.initials: L
authors.lastname: Girard
authors.forename: David E
authors.initials: DE
authors.lastname: Misek
authors.forename: Jeremy M G
authors.initials: JM
authors.lastname: Taylor
authors.forename: Samir
authors.initials: S
authors.lastname: Hanash
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Naoki
authors.forename: D Neil
authors.initials: DN
authors.lastname: Hayes
authors.forename: Christine
authors.initials: C
authors.lastname: Ladd-Acosta
authors.forename: Steven A
authors.initials: SA
authors.lastname: Enkemann
authors.forename: Agnes
authors.initials: A
authors.lastname: Viale
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Giordano
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D005240:Feasibility Studies; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D007753:Laboratories / Q000592:standards*; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis