Microarray analysis

SIGNIFICANCE: Microarray analysis is the procedure used by geneticists to place similar DNA fragments side by side for comparison. With this process, they can compare genetic structure and reactions of genetic material.

Procedure

For analysis, several hundred to millions of DNA oligonucleotides are placed on a small piece of glass, a filter, or a silicon slide. These oligonucleotides, called probes, are bonded to the substrate by a chemical. Usually the DNA is focused on several specific genes, which are lined up by number, or type. This task is performed by a robot due to its precise requirements and microscopic size. Testing on the genes can be performed simultaneously. The genes of interest are often tagged with a fluorescent substance, so that they stand out from the others and can be easily compared.

The probes can be further processed into spotted microarrays. For this type of microarray, smaller fragments of the DNA are dropped onto another glass slide. This task is performed by using needles to withdraw the DNA fragments. Both the spotted microarrays and the microarrays are then scanned using either laser or radiographic imaging.

Uses for Microarray Analysis

The scan produces a database of genetic information that can be further analyzed and tested. Microarray analysis was initially intended for pharmaceutical research. By examining the genes from a group of patients with the same condition, drug researchers can view the genetic structure and the proteins produced by these genes. With this information, researchers can use this information to target drug therapy. An example of this is the development of Herceptin for breast cancer patients who are HERS positive.

Researchers in academia now use DNA microarray analysis data to better understand disease processes. Using this data, researchers are able to describe a profile of normal genetic structure, as well as, specific genetic mutations leading to disease. This process defines the specific genetic changes (genotype) related to specific symptoms (phenotype). Some research is performed by exposing the genetic material to pathogenic organisms or to drugs, and then examining the response of the genes.

Forensic science uses genetic material from a suspected perpetrator, and compares it with DNA left on the victim. Microarrays of genetic material can be used to define specific microorganisms, such as various influenza viruses. They can be used for diagnosis of conditions caused by genetic mutations. In some conditions, the same symptoms can be caused by a variety of genetic mutations, usually within one gene.

Issues with Microarray Research

Despite the advantages of DNA microarray analysis, there are still issues that must be overcome. The first one is standardization of the microarrays. At the present time, there are a number of variables in the process of developing microarrays of DNA materials. These variables include the type of surface used, the process of fabricating the microarray and the actual analysis of the derived data. Efforts are being made to standardize microarrays. A checklist called the Minimum Information About a Microarray Experiment (MIAME) was developed, but this checklist is not complete. Currently, the US Food and Drug Administration (FDA) is developing standards and quality control for DNA microarray data.

Another issue is the normalization of DNA microarrays. Normalization facilitates the statistical analysis of the data, by organizing them into a database. This process of normalization is more complicated with microarray data due to its large numbers of records and multiple dimensions for each piece of genetic data. Some of these bits of data are irrelevant and can produce a false positive or false negative response. Statistical packages that normalize microarray data are now available.

Study design for microarray analysis must allow for of the genetic material within the microarray. Replication is required to draw valid conclusions from these studies. It provides multiple records for a single bit of genetic material. It is important that sample preparation be communicated so that summary statistics will be accurate.

Impact

Microarray analysis has revolutionized pharmaceutical and genetic research. It has given pharmaceutical researchers the ability to develop drugs that are specific to demographic groups. The ability to actually compare and contrast genes is providing new information about the source of medical conditions. Since it tests a group of genes, microarray analysis permits researchers to test large volumes of genetic material much more quickly. From this information, it is possible to test an individual for a genetic disease, verify the diagnosis, and even to predict the likely outcome of treatment.

Key terms

• nucleotidesthe two lengthy strands made of sugar and phosphate groups that form the outside structure of the DNA molecule
• oligonucleotidea fragment of a DNA sample used for microarray analysis
• probea sample of DNA which is part of a microarray

Bibliography

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Cleator, Susan J., et al. “The Effect of the Stromal Component of Breast Tumours on Prediction of Clinical Outcome Using Gene Expression Microarray Analysis.” Breast Cancer Research August 2006. Print.

Elkins, Kelly M. Forensic DNA Biology: A Laboratory Manual. Waltham: Academic Press, 2013. Print.

Emmert-Streib, Frank, and Mathias Dehmer. Analysis of Microarray Data: A Network-Based Approach. Berlin: Wiley, 2008. Print.

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