Gene expression analysis of pre-defined sets of neoplastic tissues

To identify a group of genes, characteristic of a single neoplasia and determinant for the risk to relapse, we have performed gene expression analysis of ductal breast carcinoma samples using Affymetrix oligonucletide microarray (HU133A). Biopses from 60 patients, 30 good prognosis (desease free from six to ten years after surgical treatment) and 30 poor prognosis, have been analyzed. From each group we have created six homogeneous pools to show, during the analysis, only genes expressed in a greatly different way. A reduced number of cases has been used to avoid dilution of genes expressed only in few samples. Analysis have identified 77 candidate genes with a specific ontological distribution that contained some genes that were linked to breast cancer by previous studies. Microarray results validation has been performed by real-time PCR analysis on 127 single cases of breast cancer. Gene function study and literature data allow to define our candidate genes as potential markers of prognosis. Keywords: Breast cancer gene expression analysis From a group of 130 frozen tumor samples, 30 cases of ductal invasive carcinoma with recurrence within 72 months from surgery (high-risk) and 30 without recurrence (low-risk) were selected for microarray analysis. From each group, 6 RNA pools of 5 samples each were prepared and analyzed on GeneChip Human Genome U133A oligonucleotide microarrays. Hybridizations were performed in technical duplicates, in two experimental sessions.