The linkage test is an approach to DNA testing that allows a prediction to be made about the presense of a mutated gene evenif there is, at present, no clue at all about what the gene itself is, what changes have occurred in its DNA sequence, or what function the gene serves in the cells. Linkage tests can often be used in situations in which a direct DNA test cannot be done.

What happens in a linkage test is this: When there is no way to detect the "target" gene directly, a known region of DNA located close to the target gene can be used as a "marker" for the target gene. By following the marker, predictions about the actual state of the nearby target gene can be made. The marker serves as an indicator in much the same way that the tall flag attached to a child's bicycle alerts a motorist to the presence of the child, who might be hidden from view by cars, bushes, or signs as she pedals along.

Linkage testing relies on the strong tendency of two regions of DNA that are near each other, linked together on a chromosome, to stay together when the sperm and egg cells are formed. The closer these two DNA regions are to each other on the chromosome, the more likely it is they will stay together and be inherited together. If the marker and the target gene are not very close, they can occasionally become separated from each other by the processes of chromosome breakage and exchange of pieces which occurs between members of the same chromosomic pair during egg and sperm formation. Such reshuffling of DNA regions is a normal event.

Several types of DNA markers are useful for linkage testing. One type of marker can simply be another gene which is located very close to the target gene and which produces a protein that can be measured. Keeping track of the marker gene (through its protein product) provides an important clue about whether or not the mutant gene has been inherited. If we find that the marker gene has been passed along from a parent to a child, it is a strong indication that the nearby mutant gene has also been inherited. Conversely, the absence of the marker gene is a strong indication that the mutant gene is also absent.

An even more useful kind of marker takes advantage of differences in base sequences of the DNA molecule in the vicinity of the target gene. Tiny variations in the base sequence occur at many places scattered throughout the DNA. By some estimates, a single base-pair variation along the DNA molecule occurs about once every five hundred base pairs. This means that the DNA sequence found on one chromosome can and does differ slightly from the DNA sequence of its partner chromosome. The DNA molecules of the partner chromosomes can also differ from each other in another way: Some places on the chromosomes can contain extended sequences where one type of base altnernates with another many times. These variations are generally without any harmful effects and go unnoticed by the organism, since the vast majority of them occur in those extensive "junk" DNA portions of the chromosomes.