A DNA microarray (also DNA chip or gene chip in common speech) is a piece of glass or plastic on which pieces of DNA have been affixed in a microscopic array. Scientists 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. Thousands of identical probe molecules are affixed at each point in the array to make the chips effective detectors.
Although the name GeneChip is a trademark of Affymetrix, microarray users generally use this term, or, simply, chip, to refer to any microarray, not just those sold by Affymetrix. While Affymetrix arrays use short oligonucleotide probes of 25 bases or less, many microarrays use PCR products, genomic DNAs, BACs, plasmids, or longer oligos (35 to 70 bases). Microarrays may be made by any number of technologies including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, or ink-jet printers (http://genomebiology.com/2004/5/8/R58). The use of microarrays for expression profiling was first published in 1995 (Science) and the first complete eukaryotic genome (Saccharomyces cerevisiae) on a microarray was published in 1997 (Science).
Typically arrays are used to detect the presence of mRNAs that may have been transcribed from different genes and which encode different proteins. The RNA is extracted from many cells, ideally from a single cell type, then converted to cDNA or cRNA. The copies may be "amplified" in concentration by rtPCR. Fluorescent tags are enzymatically incorporated into the newly synthesized strands or can be chemically attached to the new strands of DNA or RNA. A cDNA or cRNA molecule that contains a sequence complementary to one of the single-stranded probe sequences will hybridize, or stick, via base pairing (more at DNA) to the spot at which the complementary probes are affixed. The spot will then fluoresce (or glow) when examined using a microarray scanner.
Increased or decreased fluorescence intensity indicates that cells in the sample have recently transcribed,or ceased transcription, of a gene that contains the probed sequence ("recently," because cells tend to degrade RNAs soon after transcribing them). The intensity of the fluorescense is roughly proportional to the number of copies of a particular mRNA that were present and thus roughly indicates the activity or expression level of that gene. Arrays can paint a picture or "profile" of which genes in the genome are active in a particular cell type and under a particular condition.
Because many proteins have unknown functions, and because many genes are active all the time in all kinds of cells, researchers usually use microarrays to make comparisons between similar cell types. 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 may indicate genes that are uniquely associated with the disease. Typically in such a test, the two samples' cDNAs are tagged with two distinct colors, enabling comparison on a single chip. Researchers hope to find molecules that can be targeted for treatment with drugs among the various proteins encoded by disease-associated genes.
Although the chips detect RNAs that may or may not be translated into active proteins, scientists refer to these kinds of analysis as "expression analysis" or expression profiling. Since there are hundreds or thousands of distinct probes on an array, each microarray experiment can accomplish the equivalent of thousands of genetic tests in parallel. Arrays have therefore dramatically accelerated many types of investigations.
Microarrays are also being used to identify genetic mutations and variation in individuals and across populations. Short oligonucleotide arrays can be used to indentify the single nucleotide polymorphisms (SNPs) that are thought to be responsible for genetic variation and the source of susceptibility to genetically caused diseases. Generally termed "genotyping" applications, chips may be used in this fashion for forensic applications, rapidly discovering or measuring genetic predisposition to disease, or identifying DNA-based drug candidates.
Microarrays and bioinformatics
The lack of standardization in arrays presents an interoperability problem in bioinformatics, which hinders the exchange of array data. Many researchers use Affymetrix technology because it is popular and standardized which can simplify the comparison of results from different laboratories. At the same time, various grass-roots open-source projects are attempting to facilitate the exchange and analysis of data produced with non-proprietary chips. The MIAME(Minimal Information About a Microarray Experiment) standard for describing a microarray experiment is being adopted by many journals as a requirement for the submission of papers based on microarray results.
- http://cmgm.stanford.edu/pbrown/mguide/ - How to build your own arrayer
- http://genomebiology.com/2004/5/8/R58/ - How to build your own ink jet microarrayer
- http://microarrays.org - Protocols, how-to documents, free software
- 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.combimatrix.com - CombiMatrix is a provider of custom DNA microarrays.
- http://www.statsci.org/micrarra/ - Array links
- PLoS Biology Primer: Microarray Analysis (http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371%2Fjournal.pbio.0000015)
- http://www.mged.org/ - The Microarray Gene Expression Data Society, and home of MIAME