A gene chip is a piece of glass or plastic on which pieces of DNA, which are referred to as "probe sequences," have been affixed in a microscopic array. Machines use such chips to simultaneously screen a single biological sample for the presense of many genetic sequences.
Because "GeneChip" is a trademarked name owned by Affymetrix, scientists tend to speak and write about "gene chips" only in reference to the chips that Affymetrix makes. Brought to market in 1996, these were the first to come into use, and they are referred to generically as oligonucleotide arrays, because the probe sequences are short pieces of DNA about 10 to 50 nucleotides long. A still broader term is microarray, which refers not only to GeneChips but to chips that use much longer probe sequences, such as the entire genes that may be contained on cDNAs. Because, Affymetrix owns a patent both on the use of oligonucleotides probes as well as on the means the company uses to affix them to the chip, microarrays that are not made by Affymetrix are manufactured by a different technique that is non-proprietary.
Typically arrays are used to detect the presence of different mRNAs in an extract from a sample of cells from a single tissue. If mRNA binds to the spot on an array to which a specific probe sequence has been affixed, that implies that the cells are actively transcribing a gene with a sequence complementary to that probe (see "anti-sense" under DNA).
Researchers usually employ microarrays in a comparison between two samples. For example, an RNA sample from brain tumor cells, might be compared to a sample from healthy neurons or glia. Probes that bind RNA in the tumor sample but not in the healthy one indicate genes that are uniquely associated with the disease. Such identifications can lead to candidate targets for drugs.
Since there are hundreds of thousands of probes on a gene chip, using a gene chip can be the equivalent of thousands of conventional genetic tests. Gene chips have therefore dramatically accelerated the pace of genetic research.