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linkage analysis examination of co-inheritance of disease and DNA markers, used to locate disease genes positional cloning the use of polymorphic genetic markers ever closer to the unknown gene to track its inheritance in CF families

some of the techniques used to identify the CF gene, such as "gene walking" and "gene jumping," are no longer used extensively.

The CF gene was identified through linkage analysis and positional cloning. Whereas nowadays the map of the human genome is saturated with these markers, which serve as convenient "signposts" in gene mapping studies, this was not the case when the CF mapping was done, and more laborious, brute-force techniques such as those mentioned above had to be employed. Thus, it was dramatic news indeed when the causative gene was found on chromosome 7.

As might have been expected based on the secretory defects in the disease, the gene, dubbed "cystic fibrosis transmembrane conductance regulator" (CFTR), encodes an ion-channel protein in epithelial cell membranes. The gene is quite large—250,000 nucleotides—and the spectrum of mutations in CF patients continues to grow. At the time of this writing, more than 950 different mutations have been reported. Most of these are quite rare and may only be found in individual families. A few are more common, most notably a three-nucleotide deletion of codon 508, called AF508, which is found in approximately 70 percent of Caucasian CF carriers. Several others are present in 1 percent to 3 percent of carriers, while the remainder are very rare, except for some that are found at higher frequency in particular ethnic and racial groups (such as W1282X in the Ashkenazi-Jewish population and 3120+ 1G* A in the African-American population).

The AF508 mutation in the CFTR gene deletes a phenylalanine amino acid from the final protein. Like other membrane proteins, CFTR is made at the endoplasmic reticulum in the interior of the cell, and must be transported to the plasma membrane to function. The absence of this amino acid results in improper folding of the CFTR protein within the endoplasmic reticulum, which causes it to be degraded by the cell's protein-recycling machinery before it reaches the membrane. Some of the less common mutations prevent any protein synthesis by introducing a stop codon into the gene, while others allow the protein to reach the membrane but without functioning properly.

The CFTR protein forms a pore to allow chloride ions to pass through the plasma membrane. The full range of functions served by this pore is not known, but the sticky secretions of CF are believed to result when chloride ions in the salty fluid secreted by the epithelial cells cannot be recovered by the membrane protein.

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