Latin Square Design to Gene Expression Experiments

Tetsutaro Hamano1, Akira Ohide2, Masaru Sekijima, Kazuto Nishio, Masahiro Takeuchi, Yasuhiro Fujiwara, Division of Biostatistics, Kitasato University Graduate School, Japan;, Applied Biology Division, Kashima Laboratory, Mitsubishi Chemical Safety Institute, Japan

Replication, randomization, and local control are essential for confirmatory gene expression experiments, notably in clinical research. We used a randomized Latin square design for blocking experimental variations and for estimating tamoxifen effect in human breast cancer cell lines assay. Orthogonal decomposition of a gene expression map based on the experimental design is expected to elucidate treatment effects as well as systematic error components, which can be used to further model and normalize the gene expression data. To examine the tamoxifen effect, gene arrays on nylon membranes (Clontech Atlas Gene Arrays) were used. Although single color gene expression assays were used in our experiment, this design can be equally beneficial for other settings where two color spotted cDNA microarrays are used.