Preece, Christina

498 Background: Prior study, demonstrating differential immunohistochemical EGFR expression between the primary colon cancer and the liver metastasis, suggested possible molecular differences between the two tumor sites. This questions the relevance of obtaining genomic information from the primary tumor to guide adjuvant treatment. In this study we examine whether there are genomic differences specific to metastatic nodes versus the paired colon primary samples. Methods: Using 30 primary and lymph node metastasis pairs (dissected for >80% tumor from paraffin embedded tissue), we obtained a dataset of copy number derived from the Affymetrix Oncoscan Molecular Inversion Probe platform. Using the Nexus Copy Number software for processing, we used the default automatic segmentation of the copy number data with a threshold for calling copy number gains/losses of 2.3/1.7. Subsequently we applied the Wilcoxon signed-rank test in order to find regions showing copy number imbalance that differ between the paired nodes and tumors correcting for multiple comparisons by performing permutation-based estimation of the false discovery rate permuting the samples 100 times. Results: Using 40 ng of total DNA from paraffin embedded tumor from primary and tumor in positive nodes, we obtained high quality, genome wide copy number data. Using FDR < 0.1, we identified four chromosomal segments that showed statistically significant increased likelihood of copy number gains in the primary tumor compared to the tumor-containing node. Thirty five percent of tumor-bearing lymph nodes were copy number normal at the EGFR locus whereas the corresponding primary tumor showed amplification at 7p11.2 (includes the EGFR gene). A similar pattern was observed for 8q24, 14q11.2, and 20q12-q13; regions associated with aggressive tumor behavior. Conclusions: Our results demonstrate four significant differences between the primary tumor and lymph node metastasis and in all cases the metastasis were copy number normal compared to the copy number gain observed in the primary tumor. These results support the importance to examine differences at the genome level between the metastatic tumor site and the primary.