title: Optimization of an animal test protocol for toxicogenomics studies (ii); a cross-laboratory gene expression analysis.
abstract: Toxicogenomics is a promising new tool for prediction of chemical toxicities including carcinogenicity in a relatively short period. However, it is important to develop a reliable animal test protocol for toxicogenomics studies. The preparation of RNA and tissues is also crucial, since it greatly influences outcomes of gene expression analysis. We proposed an animal test protocol for toxicogenomics studies. In the present study, we examined an animal test protocol by comparing biological and gene expression data from different laboratories running identical in vivo studies on the same microarray platform. The results gave good correspondence in all three laboratories at the level of biological responses and gene expression, especially for genes whose expression changes were quite large. As the fold change or the signal values become smaller, however, discrepancies occur in gene expression data. For example, one laboratory shows an opposite directional change to the other two or no change. The results of hierarchical clustering and principal component analysis (PCA) demonstrated all samples from the three laboratories being clearly divided between control and treatment. Examination of the reproducibility of gene expression data across laboratories using the proposed animal test protocol thus confirmed only minor differences, which was expected to present no problems for gene expression analysis.
authors.affiliation: Sumitomo Chemical Co., Ltd., 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-8558, Japan. sumida@sc.sumitomo-chem.co.jp
authors.forename: Kayo
authors.initials: K
authors.lastname: Sumida
authors.forename: Koichi
authors.initials: K
authors.lastname: Saito
authors.forename: Kenji
authors.initials: K
authors.lastname: Oeda
authors.forename: Masanori
authors.initials: M
authors.lastname: Otsuka
authors.forename: Kazunari
authors.initials: K
authors.lastname: Tsujimura
authors.forename: Hideki
authors.initials: H
authors.lastname: Miyaura
authors.forename: Masaru
authors.initials: M
authors.lastname: Sekijima
authors.forename: Koji
authors.initials: K
authors.lastname: Nakayama
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Kawano
authors.forename: Yuki
authors.initials: Y
authors.lastname: Kawakami
authors.forename: Makoto
authors.initials: M
authors.lastname: Asamoto
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Shirai
mesh_terms: D000818:Animals; D015197:Carcinogenicity Tests / Q000379:methods*; D020869:Gene Expression Profiling; D007753:Laboratories / Q000592:standards / Q000706:statistics & numerical data; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D015203:Reproducibility of Results; D012107:Research Design; D043922:Toxicogenetics / Q000379:methods*