For many genes with important functions, no associated protein product is yet known. The biochemical bases of many human genetic diseases, for example, are still unknown. How can these genes be isolated? One approach is to first determine the general location of the gene on the chromosome by using recombination frequencies derived from crosses or pedigrees (see Chapter 5). After the chromosomal region where the gene is found has been pinpointed, genes in that region can be cloned and identified. Then other techniques can be used to determine which of the “candidate” genes might be the one that causes the disease. This approach—isolation of genes on the basis of their position on a gene map—is called positional cloning.

In the first step of positional cloning, geneticists use mapping studies (see Chapter 5) to establish linkage between molecular markers and the phenotype of interest. Demonstration of linkage between the phenotype and one or more molecular markers provides information about which chromosome carries the locus that codes for the phenotype and its general location on that chromosome. The next step is to narrow down the location of the locus by using additional molecular markers clustered in the chromosomal region where the locus resides.

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After the locus has been mapped, clones that cover the region can be isolated from a genomic library and all genes located within the region can be identified. Genes can be distinguished from other sequences by the presence of characteristic features, such as consensus sequences in the promoter and start and stop codons within the same reading frame. After candidate genes have been identified, they can be evaluated to determine which is most likely to be the gene of interest.

The expression pattern of the gene—where and when it is transcribed—can often provide clues about its function. For example, genes for neurological disease would probably be expressed in the brain. Geneticists often look in the coding region of the gene for mutations among people with the disease. More will be said about determining the function of genes in the sections that follow and in Chapter 15.