In 1999, the National Cancer Institute (NCI) began a funding initiative called the Director's Challenge: Toward a Molecular Classification of Tumors, with the goal of defining comprehensive profiles of molecular alterations in tumors that could be used to identify subsets of patients. These molecular profiles would provide the basis for future studies to validate the clinical utility of molecular-based classification schemes. A further goal of this initiative was the development and implementation of a plan for the timely release of the extensive data sets expected to result from these projects. At that time, it was becoming apparent that the knowledge of the entire human genome combined with rapidly improving technology for comprehensive analysis of the 20,000 to 25,000 genes and encoded proteins would provide an opportunity for a deeper understanding of the molecular basis of disease processes that would guide the evolution of improved therapies based on new diagnostic schemes. Specific molecular profiles correlate with important clinical parameters,which should allow physicians to base management decisions on the molecular characteristics of an individual patient's tumor, and improve a physician's ability to determine the primary tumor site for tumors of unknown origin at the time of their detection.
With the development and application of DNA micro-arrays, the expression of almost all human genes now can be systematically examined in human malignancies. This has led to the identification of candidate molecular targets for therapeutic intervention and biomarkers for early detection of these diseases. Various studies have demonstrated that patterns of gene expression can distinguish between tumors of different anatomic origin and define new subgroups of cancers with similar histologic appearances but distinct molecular profiles. Some of these new molecular subclasses of tumor appear to correlate with clinical behavior. Tests for characteristic gene expression patterns have not yet been translated into routine use in the clinical molecular laboratory and are unlikely to replace conventional microscopy in the near future. It is clear, however, that the practice of surgical pathology will significantly change as these findings are able to be incorporated into daily use. Instead of translation of findings from "bench to bedside," as in clinical oncology, discoveries will be translated from "bench to microscope."
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