Gene Profile Analysis of Archived Tumors -Total Cancer Care (TCC) Database

We identified 10,240 genomically profiled distinct solid, primary, non-metastatic tumors from the TCC database, a prospective IRB-approved tissue collection protocol active at the Moffitt Cancer Center and 17 other institutions since 2006.(20) Tumors from patients enrolled in the TCC protocol were arrayed on Affymetrix Hu-RSTA-2a520709 Gene Chips (Affymetrix, Santa Clara, CA). The chip contains roughly 60,000 probesets representing 20,155 unique genes. Iterative Rank-Ordered Normalization (IRON) was used to normalize all samples and log2 values were calculated.(21). A RNA quality batch effect was removed using Partial Least Squares. Both the normalized and de-batched expression values for 10,240 tumor samples from the ten RSI genes and 12 chemokine genes were extracted from the TCC database.