Microarray Data Analysis

Cancer is a genetic malady, mostly resulting from acquired mutations and epigenetic changes that influence gene expression. Accordingly, a major focus in cancer research is identifying genetic markers that can be used for precise diagnosis or therapy. Over the last half-century, investigators have used reductionism to discover such markers through the study of simple genetic changes, like balanced chromosomal translocations. For example, fundamental insights into the nature of the bcr-abl gene translocation product resulted in the precise molecular classification of chronic myelogenous leukemia and recently led to the development of the molecularly targeted tyrosine kinase inhibitor STI571 (Gleevec; Novartis, East Hanover, NJ, USA) for the treatment of this disease. Ninety percent of human cancers, however, are epithelial in origin and display marked aneuploidy, multiple gene amplifications and deletions, and genetic instability, making resulting downstream effects difficult to study with traditional methods. Because this complexity probably explains the clinical diversity of histologically similar tumors, a comprehensive understanding of the genetic alterations present in all tumors is required.