Comparative genomic hybridization data and web-based tool for the NCI-60

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Array-based comparative genomic hybridization (aCGH) is a powerful technique for detecting gene copy number variation. It is generally considered to be a less variable parameter than gene expression since it measures the more consistent DNA, rather than the condition dependent and labile RNA. In the current study, we combine copy number estimates from four different platforms (Agilent 44K, Nimblegen 385K, Affymetrix 500K and Illumina Human1Mv1_C) to compute a high-resolution measure of copy number changes in the 60 cancer cells of the NCI-DTP (the NCI-60). We will plan to release that database on CellMiner (http://discover.nci.nih.gov/cellminer), the host for our web-based tools. This should facilitate easy access, interpretation and comparison of this information to our pre-existing transcript expression data for 26,065 genes and 360 microRNAs, and the activity of 20,602 compounds and drugs for the scientific community. Initial comparisons of copy number and expression levels indicates an overall medium correlation (median r=0.247), with significantly higher correlations (median r=0.408) for the known tumor suppressor genes. This is consistent with gene loss being an important mechanism for tumor suppressor inactivation. Using the parameter of the focal nature of the DNA gains or losses, in tandem with changes in transcript expression, it may be used to identify novel candidate tumor suppressors.