The process of determining an individual's genetic polymorphisms is known as genotyping. One of the earliest methods used in genotyping looked not at genes but at polymorphic proteins known as isoenzymes, or isozymes. Isoenzymes are different forms of a protein, with slightly different amino acid compositions. Since a protein's amino acid composition is genetically programmed by the DNA sequence that encodes it, analysis of isoenzymes surveys genetic polymorphism. Because these differences in amino acid composition can cause proteins to have different electrical charges, isoenzyme polymorphisms are assessed by extracting an organism's proteins and separating them using gel electrophoresis—a technique also used to study DNA polymorphisms.
In gel electrophoresis, an electric field is applied across a gel matrix, and molecules move through the matrix in response to the electric field. The gel matrix is a porous material, similar to Jell-O, that acts as a sieve and slows down large molecules more than small molecules. Isoenzymes move through the gel matrix according to their electrical charge and size, and are separated from each other on this basis. In this way, different isoenzymes can be identified.
Many tools for assessing DNA polymorphisms are now available. Some of these methods assess length polymorphism (indels), sequence polymorphism (base changes or rearrangements), or combinations of the two. DNA sequencing reveals all types of polymorphisms but is costly and labor-intensive. Gel electrophoresis is used in DNA analysis to both separate and sequence DNA. PCR (polymerase chain reaction) is frequently employed beforehand to produce large quantities of the DNA to be analyzed.