APPLICATIONS OF MICROARRAY

Genomics

Gene expression profiling Genotyping Array comparative genomic hybridization (aCGH)

Proteomics Profiling of biomarkers Analysis of protein activities Autoimmune and inflammatory disease detection Allergy screening Other applications In situ hybridization (ISH) Fluorescence in situ hybridization (FISH)

gene expression profiling measures the activity of thousands of genes at once, creating a global picture of cellular function. These profiles can distinguish between cells that are actively dividing, for example, or show how the cells react to a particular treatment. Many experiments of this sort measure an entire genome simultaneously, that is, every gene present in a particular cell. Microarray technology[1] measures the relative activity of previously identified target genes. Tag-based techniques, like serial analysis of gene expression (SAGE, SuperSAGE) are also used for gene expression profiling. They have two main advantages. First, they are more accurate. Second (especially SuperSAGE) they can measure any active gene, not just a predefined set. Microarrays are commercially available and more common, accounting for more than 95% of the expression profiling papers published in the last year according to a recent PubMed search.

The academic research community stands to benefit from microarray technology just as much as the pharmaceutical industry. The ability to use it in place of existing technology will allow researchers to perform experiments faster and more cheaply, and will enable them to concentrate on analyzing the results of microarray experiments rather than simply performing the

experiments. This research could then lead to a better understanding of the disease process. While the field of expression has received most attention so far, looking at the gene copy level and protein level is just as important. Microarray technology has potential applications in each of these three levels. Identifying drug targets provided the initial market for the microarrays. A good drug target has extraordinary value for developing pharmaceuticals. By comparing the ways in which genes are expressed in a normal and diseased heart, for example, scientists might be able to identify the genes and hence the associated proteins -- that are part of the disease process. Researchers could then use that information to synthesize drugs that interact with these proteins, thus reducing the disease's effect on the body. Gene sequences can be measured simultaneously and calculated instantly when an ordered set of DNA molecules of known sequence a microarray is used. Consequently, scientists can evaluate an entire set of genes at once, rather than looking at physiological changes one gene at a time. For example, Genetics Institute, a biotechnology company in Cambridge, Massachusetts, built an array consisting of genes for cytokines, which are proteins that affect cell physiology during the inflammatory response, among other effects. The full set of DNA molecules contained more than 250 genes. While that number was not large by current standards of microarrays, it vastly outnumbered the one or two genes examined in typical pre-microarray experiments. The Genetics Institute scientists used the array to study how changes experienced by cells in the immune system during the inflammatory response are reflected in the behavior of all 250 genes at the same time. This experiment established the potential for using the patterns of response to help locate points in the body at which drugs could prove most effective.

1. Microarray technology will help researchers learn more about many different diseasesheart disease, mental illness, and infectious disease, to name only a few. 2. Cancer studies: One intense area of microarray research at the NIH is the study of cancer. In the past, scientists have classified different types of cancer based on the organs in which the tumors develop. With the help of microarray technology, however, they will be able to further classify these types of cancer based on the patterns of gene activity in the tumor cells and

will then be able to design treatment strategies targeted directly to each specific type of cancer. 3. Additionally, by examining the differences in gene activity between untreated and treatedradiated or oxygen-starved, for example tumor cells, scientists can better understand how different types of cancer therapies affect tumors and can develop more effective treatments. 4. Gene Expression: A new way of studying how large numbers of genes interact with each other and how a cell's regulatory networks control vast batteries of genes simultaneously. 5. Mutational studies: Although it is known that mutations, or alterations in a genes DNA, result in certain diseases, it is often difficult to identify and characterize these mutations because most large genes have many regions where a mutation could occur and cause disease. Examples of such genes are BRCA1 and BRCA2, which are believed to cause as many as 60% of all cases of hereditary breast and ovarian cancers. In BRCA1 alone, over 500 different mutations have already been discovered. The DNA microchip is a revolutionary new tool used to identify mutations in genes like BRCA1 and BRCA2. To determine whether an individual possesses a mutation for BRCA1 or BRCA2, a scientist first obtains a sample of DNA from her blood, as well as a sample that does not contain a mutation in either gene. After denaturing, or separating the samples of DNA into single strands, and cutting the them into smaller, more manageable fragments, the researcher labels the fragments with fluorescent dyes. The individuals DNA ( isolated from cancerous cells) is labeled

with green dye and the normal DNA is labeled with red dye. Both sets of labeled DNA are then inserted into the chip and allowed to hybridize, or bind, to the synthetic BRCA1 or BRCA2 DNA on the chip. If the individual does not have a mutation for the gene, both the red and green samples will hybridize with the sequences on the chip. If the individual does possess a mutation, the red (normal) DNA will still hybridize perfectly with the DNA on the chip, but the green (individuals) DNA will not hybridize properly in the region where the mutation is located. The scientist can then examine this area more closely to confirm that a mutation is present.