Whole breast tissue gene expression in comparison to expression in epithelial and stromal tissues

The breast tissue contains both epithelial and stromal tissues in its composition. In this substudy we compared the gene expression of the whole core needle biopsy of the breast with the expression observed in its epithelia and stroma. Laser capture microdissection was performed to compare the gene expression profile in the whole breast biopsy with that in the epithelial and stromal tissues. In this study we had samples collected from nive premenopausal women, free of any breast abnormality. For each of nine women included in this substudy, three microarrays were performed in the same batch, using RNA extracted from 1) the epithelial cells of the mammary gland, 2) the stroma and 3) whole tissue. For each subject a linear regression model was fitted across all genes. The gene expression values in the whole tissue were modeled as a linear function of the gene expression in epithelial and stromal tissues.