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Tools and Equipment of Science

Author(s): Tracy Volz, PhD
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Gene Discovery by Linkage Analysis

Many genes have been discovered by an approach called linkage analysis. Linkage analysis relies on Mendelian inheritance of chromosomes (and genes). In linkage analysis, polymorphic genetic markers (sites of DNA sequence variations) spread throughout the genome are used to track the transmission of various genomic regions through a family. With linkage analysis, all members of a family are genotyped for the polymorphic markers. The genotype of each family member at each marker is then compared to the genotypes of other family members to determine which markers are present in the family members affected by the disorder. Since linkage analysis does not detect mutations in genes directly, but rather traces a potential disease allele through a family because of a tight association (genetic linkage) between the potential disease gene and the marker, further investigation is required once a genomic region of interest is identified. The goal of the investigation is to identify the gene and mutations associated with the disorder. Since linkage analysis is not a direct mutation detection method, its level of sensitivity relies on how many different forms of the markers there are, the density of the markers throughout the genome, and the genetic distance between the marker and the disease gene. Highly polymorphic markers, and lots of them, improve the success rate of linkage analysis.

Linkage analyses must be performed with data sets based on large, multigenerational families. This is because one needs many individuals, and typically more than one affected individual, within a family to identify the genomic regions associated with a disorder with statistical significance. However, large families segregating genetic disorders are not always easy to find, especially in highly mobile societies like the United States. In some cases, a several small families can be used instead, but this approach requires that the disease is caused by the same gene in all the families. For example, if the disorder is caused by mutations in the same gene in every individual affected by the disorder, then the results of linkage analysis of many small families can be added together because everyone affected by the disorder should share the same disease gene. One example of such a disorder is cystic fibrosis (CF), in which all individuals affected by the disorder have mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). On the other hand, if a disorder is caused by mutations in more than one gene, linkage analysis will be more successful if large, multigenerational families are used because two different families might have the disease because of mutations in different genes. In these cases, the linkage data would appear contradictory and would not be additive. One example of a highly heterogeneous genetic disorder is nonsyndromic hearing loss. More than 100 genes have been mapped so far for hereditary deafness.

Genetic heterogeneity has complicated the search for the genetic factors associated with a number of common complex disorders such as schizophrenia and autism. In these disorders, multiple genetic factors are likely to be involved and each may have only a small effect on susceptibility to develop the disorder. As such, the disorder in any two families may be associated with different sets of genes. Sorting out the genetic factors involved is quite complicated and requires extensive additional investigations.

As a result of the Human Genome Project, researchers now have a collection of polymorphic genetic markers that provide excellent coverage of the genome. These markers are powerful tools for mapping disease genes. Linkage analysis strategies are precise, accurate and effective, but labor intensive. However, while they often require data from large families, they do not require an investigator to know anything about the underlying biochemical mechanisms involved in the disorder.

In the simplified diagram on this slide, a polymorphism associated with an autosomal recessive disorder is indicated by the red star. Only the affected individual has inherited two copies of the disease-associated polymorphism. From this finding, researchers would explore the genetic region surrounding the marker to identify genetic alterations unique to the disease-associated form of the marker.