Study to evaluate the effect of the type of tissue on gene expression measurements

To evaluate the effect of tissue type (cytology vs. surgical tissue) on gene expression measurements. Information was used to select probesets with a high spatial reproducibility for the development of gene signatures. 88 breast cancer samples were obtained at the time of surgery prior to any systemic treatment. In addition to a solid tissue sample, a scrape (=cytology) sample was taken by scraping with a scalpel over the cut-surface of the tumor. Samples were stored in RNAlater and profiled on Affymetrix U133A microarrays.