Gene expression studies on breast cancer have generally been performed on tissue obtained at the time of surgery. In this study, we have compared the gene expression profiles in preoperative tissue (core needle biopsies) while tumor is still in its normal milieu to postoperative tissue from the same tumor obtained during surgery. Thirteen patients were included of which eleven had undergone sentinel node diagnosis procedure before operation. Microarray gene expression analysis was performed using total RNA from all the samples. Paired significance analysis of microarrays revealed 228 differently expressed genes, including several early response stress-related genes such as members of the fos and jun families as well as genes of which the expression has previously been associated with cancer. The expression profiles found in the analyses of breast cancer tissue must be evaluated with caution. Different profiles may simply be the result of differences in the surgical trauma and timing of when samples are taken and not necessarily associated with tumor biology. 1. Introduction Breast cancer is detected either by clinical signs such as palpable tumour or in mammographic screening. In both cases biopsies are taken from the tumour to determine whether the tumour is benign or malign. If malignancy is detected, the patient will be scheduled for surgery within a few weeks. Before the surgery, sentinel node (SN) diagnostics is generally performed to examine the spread of cancer cells to axillary lymph nodes. The SN can be identified using a blue dye, a radioactive colloid, or a combination of the two [1, 2]. Microarray technology enables scientists to study thousands of genes simultaneously. The resulting molecular profile can be used to study complex multifactorial diseases such as breast cancer [3, 4]. Gene signatures have been shown to correlate with clinically relevant clinicopathological parameters and prognosis [5–7]. These molecular signatures may be used to predict the individuals for whom therapy is beneficial and spare unnecessary treatment for over 80% of the others [6, 8–10]. The time of procurement, which refers to the point of when the biopsies are taken [11] as well as the postoperative handling [12], has been found to be a confounding factors in microarray data analysis in breast cancer. Most of the previously published studies consist of tumour tissue taken in connection to surgery. Biopsies taken from the tumour, while the tumour is within the breast prior to any manipulation, must be as near to the true expression state as possible. In this
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