Types of Microarrays

There are three basic types of samples that can be used to construct DNA microarrays, two are genomic and the other is "transcriptomic", that is, it measures mRNA levels. What makes them different from each other is the kind of immobilized DNA used to generate the array and, ultimately, the kind of information that is derived from the chip. The target DNA used will also determine the type of control and sample DNA that is used in the hybridization solution.

Changes in Gene Expression Levels

Determining the level, or volume, at which a certain gene is expressed is called microarray expression analysis, and the arrays used in this kind of analysis are called "expression chips". The immobilized DNA is cDNA derived from the mRNA of known genes, and once again, at least in some experiments, the control and sample DNA hybridized to the chip is cDNA derived from the mRNA of normal and diseased tissue, respectively. If a gene is overexpressed in a certain disease state, then more sample cDNA, as compared to control cDNA, will hybridize to the spot representing that expressed gene. In turn, the spot will fluoresce red with greater intensity than it will fluoresce green. Once researchers have characterized the expression patterns of various genes involved in many diseases, cDNA derived from diseased tissue from any individual can be hybridized to determine whether the expression pattern of the gene from the individual matches the expression pattern of a known disease. If this is the case, treatment appropriate for that disease can be initiated.

As researchers use expression chips to detect expression patterns— whether a particular gene(s) is being expressed more or less under certain circumstances—expression chips may also be used to examine changes in gene expression over a given period of time, such as within the cell cycle. The cell cycle is a molecualr network that determines, in the normal cell, if the cell should pass through its life cycle. There are a variety of genes involved in regulating the stages of the cell cycle. Also built into this network are mechanisms designed to protect the body when this system fails or breaks down because of mutations within one of the "control genes", as is the case with cancerous cell growth. An expression microarray "experiment" could be designed where cell cycle data are generated in multiple arrays and referenced to time "zero". Analysis of the collected data could further elucidate details of the cell cycle and its "clock", providing much needed data on the points at which gene mutation leads to cancerous growth as well as sources of therapeutic intervention.

In the same way, expression chips can be used to develop new drugs. For instance, if a certain gene is overexpressed in a particular form of cancer, researchers can use expression chips to see if a new drug will reduce overexpression and force the cancer into remission. Expression chips could also be used in disease diagnosis as well, e.g., in the identification of new genes involved in environmentally triggered diseases, such as those diseases affecting the immune, nervous, and pulmonary/respiratory systems.

http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html