Integromic analysis of the NCI-60 cancer cell lines

Abstract

Microarray-based transcript profiling has become exceedingly popular, particularly for breast cancer. However, other 'omic' profiling technologies at the DNA, RNA, protein, functional, and pharmacological levels are also becoming increasingly practical. We define 'integromics' as the melding of such diverse types of data from different experimental platforms. The whole can sometimes be more than the sum of its parts. We describe here a set of integromic studies in which we have profiled the 60 human cancer cell lines (the NCI-60) used by the National Cancer Institute to screen >100,000 chemical compounds over the last 13 years. Patterns of potency in the screen can be mapped into molecular structures of the compounds or into molecular characteristics of the cells. Here we discuss conceptual and experimental aspects of the profiling, as well as a number of bioinformatic computer programs (CIMminer, MedMiner, MatchMiner, and GoMiner) that we have developed for biological interpretation of the profiles. As briefly reviewed here, we have used the combination of NCI-60 data types to identify markers for distinguishing tumor types and to obtain pharmacogenomic clues for possible individualization of a cancer therapy.