Published in Cancer Detection and Prevention 2000; 24(Supplement 1).

Microarrays and DNA chip technology

JN Weinstein MD PhD

National Cancer Institute, Bethesda, Maryland 20892, USA,

AIM: To describe how microarray technologies can be used for molecular characterization of cancer cells at the DNA, RNA, and protein levels. Since there are 50,000 - 100,000 human genes and an even larger number of significant protein states and mutations of the DNA, it will be necessary to use high-throughput, highly multiplexed 'omic' methods (Weinstein, Science 282: 628, 1998) if we are to understand the complex molecular machinery of the cancer cell. METHODS: Chips and arrays are being made in dozens of different ways by dozens of different companies and institutions. The two most popular methods currently are based on robotic spotting of thousands of different cDNAs and on light-directed oligonucleotide synthesis. RESULTS: For purposes of illustration, the results of one gene expression study on cancer cell types from 8 different organs will be presented (for data see Ross, et al., Nature Genetics 24: 227, 2000 and Scherf, et al., Nature Genetics 24: 236, 2000). Analysis of gene expression data is a major challenge and a bottleneck in these types of studies. A useful tool for visualization of patterns in such data is the color-coded 'clustered image map' (CIM) (see Weinstein, et al., Science 275: 343, 1997). CONCLUSIONS: (1) The chip and microarray technologies, particularly those for gene expression profiling, are still immature. Results obtained from them must be treated with caution unless validated by independent means. (2) Nonetheless, important results for characterization, classification, prevention, and treatment of cancers are being achieved in a number of laboratories and institutions.

KEY WORDS: microarray, chip, protein, cancer, gene expression, prognosis, diagnosis, therapy, clustered image map.

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Paper presented at the International Symposium on Impact of Biotechnology on Cancer Diagnostic & Prognostic Indicators; Geneva, Switzerland; October 28 - 31, 2000; in the section on molecular detection & therapy.