DNA microarray

A DNA microarray (also DNA chip or gene chip in common speech) is a piece of glass or plastic on which single-stranded pieces of DNA have been affixed in a microscopic array. Machines use such chips to screen a biological sample for the presence of many genetic sequences at once. The affixed DNA segments are known as probes.

Because the name "GeneChip" is trademarked by Affymetrix[?], microarray users tend to speak and write about "gene chips" only in reference to Affymetrix chips. Made available in 1996, gene chips were the first arrays to come into use. Generically they are known as oligonucleotide arrays, because the probes they use are short segments of DNA about 10 to 50 nucleotides long.

"Microarray" refers not only to GeneChips but also 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 oligonucleotide probes as well as on a means to affix them to chips, microarrays not made by Affymetrix are manufactured by a different technique that is non-proprietary.

Typically arrays are used to detect the presence of mRNAs that encode different proteins. The RNA is extracted from many cells of a single type, then converted to cDNA and "amplified" in concentration by reverse transcriptase-PCR. Fluorescent tags are chemically attached to the strands of DNA. A cDNA molecule that contains a sequence complementary to one of the single-stranded probes will stick via base pairing (more at DNA) to the spot on the array where the probe is affixed. The spot will fluoresce (glow) when examined.

The glow indicates that cells in the sample were actively transcribing a gene that contained the sequence being probed. The intensity of the glow depends on how many molecules of a particular were present and roughly indicates the activity or expression level of a particular gene.

Researchers usually employ microarrays for 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. Typically tags of different colors are attached to the cDNAs from the two samples, enabling comparison on a single chip. Among the various proteins encoded by disease-associated genes, researchers hope to find molecules that could be therapeutically targeted with drugs.

Although the chips detect RNAs and not proteins, many scientists refer to these kinds of analysis as "expression analysis" or expression profiling[?]. Since there are hundreds of thousands of probes on an array, each can accomplish the equivalent of thousands of genetic tests in parallel. Arrays have therefore dramatically accelerated many types of investigations.

The lack of standardization in non-commercial arrays presents an interoperability problem[?] in bioinformatics, which hinders the exchange of array data. Many researchers use Affymetrix technology to a large extent because it is popular and standardized. At the same time, various grass-roots open-source projects are attempting to fascilitate the exchange and analysis of data produced with non-proprietary chips.

Links:

• http://cmgm.stanford.edu/pbrown/mguide/ - How to build your own arrayer
• http://www.genome.gov/page.cfm?pageID=10000533 - short but substantial rundown of microarray technology
• http://industry.ebi.ac.uk/~alan/MicroArray/ - the EBI is heavily involved in standardization questions concerning microarray data
• http://www.affymetrix.com
• http://www.statsci.org/micrarra/ - Array links