Gene Mapping. In the early history of gene mapping, a gene could at best be mapped to a chromosome. And now recently, due to the availability of DNA markers, genes can be mapped to a more precise site on a chromosome. The first mapping was to the X chromosomes because of the unique pattern of inheritance of X linked traits.

A big jump forward was experienced when somatic cell hybrids could be produced between human and rodent (usually mouse or hamster) cells. In these hybrid cell lines, the human chromosomes were selectively lost thereby leaving only a few human chromosomes. Mutant rodent cells were selected which were unable to make an enzyme hypoxanthine guanine phosphoribosyl transferase (HPRT) an X linked gene which the human cells could make. HPRT is required for de novo synthesis of purines. After cell fusion, the hybrid cells were grown in media containing hypoxanthine, aminopterin (inhibitor of purine and pyrimidine synthesis) and thymidine (HAT media). This ensured the growth of the hybrids with a human X chromosome (plus any others) and selected against the parental rodent strain deficient in HPRT. The human cells were often leukocytes which can be "floated off" since they do not attach and which do not have long term growth potential.

Human cell lines with structural changes were used to form the hybrid cell lines . Genes were mapped by noting which residual human chromosomes were present in independent somatic cell hybrid cultures expressing certain human gene products. For example, all cell clones that produced hexoseaminidase A, the enzyme deficient in Tay Sachs disease, had chromosome 15 regional mapping could be done using cell lines with structural changes in chromosome 15 until a more specific location could be identified.

In situ hybridization of complementary DNA or RNA was used to locate the rRNA genes. The gene probes were labeled with tritium labeled thymidine originally and later used fluorescent tags. This method can amp genes to with 1 to 2 Mb along a metaphase chromosome.

Genes near one another are said to be linked. The closer together two loci are, the more frequently they are inherited together and, conversely, the farther apart they are, the more frequently they will segregate independently. Mendel saw only independent assortment of the genes he studied because they were very far apart on the pea plant chromosomes. Genes that are very close together are said to be in "linkage disequilibrium." Genes on the same chromosome, whether or not they are linked, are said to be "syntenic.

Genes on different chromosomes, on different arms of the same chromosome or just very far apart assort independently and have a recombination frequency of 50% (0.50). Therefore, the maximum recombination frequency is 50% and recombination map distances are based on this. If two loci are found to have a recombination frequency of 5%, then they are given a map distance of 5 cM or centiMorgans. CentiMorgans were named after a famous geneticist who first described recombination in Drosophilia, a favorite of early geneticists. Recombination experiments allow one to align the genes on a chromosome in linear order. However, the physical distance is not in total agreement with the recombination distances.

The process used to determine whether two loci (disease gene and marker gene) are linked is to determine if the two (or more) loci are inherited together within a multi generational family carrying the disease gene. To determine the linkage, one makes two assumptions: 1. that the two loci are linked and 2. that they are not linked. The probability of linkage is defined as the LOD score. LOD is derived from "Log of the Odds"-of linkage. Linkage is favored if the LOD score is 3 or above. A LOD score of 3 mean it is 1000 times more likely that the two loci are linked than that they are not linked. The log of 1000 is 3, hence the LOD score of 3. A LOD score is calculated for each different recombination fraction from < 0.05 to 0.50 (maximum). More than one marker loci can be tested in the same experiment if their sequence relative to one another is known, this is called a multilocus analysis. Computer programs are available to handle the data from large linkage studies.

The Human Genome Project began in 1990 and was expected to be completed before the year 2003 but it was completed in 2000....ahead of schedule. It is an international effort to map all the human chromosomes and also the chromosomes of other organisms. Many genes and gene alignments (synteny) are common among organisms. The Human Genome Project has provided a plethora of markers along each chromosome. These markers can be used to map disease genes if they are linked to a marker (another gene, an RFLP, STR, etc.) whose location is known. The HGP goals are to identify all the estimated 30,000-120,000 genes in human DNA; to determine the sequences of the 3 billion bases in human DNA (this is essentially complete); to store this information in databases; to develop tools for data analysis; to address the ethical, legal, and social issues (ELSI) that may arise from the project.
 

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