The science of genomics faces two major quantitative challenges. First, there are very large numbers of genes in eukaryotic genomes. Second, there are myriad distinct patterns of gene expression in different tissues at different times. For example, the cells of a skin cancer at its early stage may have a unique mRNA "fingerprint" that differs from those of normal skin cells and cells from a more advanced skin cancer. In such a case, the pattern of gene expression could provide invaluable information to a clinician trying to characterize a patient's tumor.
Patterns of gene expression can be analyzed with a thumbnail-sized invention called a DNA microarray ("gene chip"), one of the most powerful new tools to emerge from genome studies. A DNA microarray is made with thousands of DNA sequences attached to the microarray in a grid pattern. The attached sequences act as probes and tell a researcher whether a test sample contains a particular DNA or RNA sequence.
DNA microarray technology is popping up in a variety of applications around the world. Each time the technology is applied to a biological question, it typically replaces a much slower, more expensive method of obtaining answers, or it simply opens up a totally new avenue of inquiry.
In the accompanying animation, we presented an application in which the gene expression profile of a cancerous tissue was compared to that of a normal tissue. Researchers are currently performing this type of experiment on an enormous range of cancers—cancers of the breast and prostate, for example, and cancers that may be either relatively benign or aggressive.
As researchers are placing cancers into more specific categories (based on gene expression profiles), they are also cataloging the relative success or failure of a patient's treatment strategy. As this bank of information grows, it will become an invaluable resource to patients and doctors. In the future, a doctor may be able to read a cancer's gene expression profile and then know immediately which treatment strategy will work the best.
As another example of this technology, a company in France recently announced that it will use DNA chips to test drinking water safety. The DNA chips for this purpose are made with gene sequences from a variety of disease-causing microbes. To perform this procedure, researchers isolate microbes from a sample of water, extract and label the DNA of the microbes, and then incubate the labeled DNA with the DNA chips. A specific fluorescence pattern on the chip indicates that a particular species of microbe is present in the water. With this technology, the company can quickly test for a number of species at the same time, rather than performing individual, time-consuming tests for each species.
Textbook Reference: Concept 13.3 Genes Come from Various Sources and Can Be Manipulated