Microsatellite haplotypes for cystic fibrosis: mutation frameworks and evolutionary tracers

Highly informative intragenic microsateilite markers within the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene allow the analysis of associations between specific mutations and haplotypes. We have analysed 440 Spanish CF families carrying 22 different CF mutations and have established haplotypes in 1, 036 chromosomes for microsatellites IVS8CA, IVS 17BTA and IVS17BCA. No new alleles were detected at the three CFTR microsatellites, in more than 3, 000 meiosis analysed (estimated mutation rate of less than 3.3×10−4). The evolution of 16 haplotypes associated with the most common CF mutation, ΔF508, and the low mutation rate at these microsateilite loci suggest that ΔF508 originated within the 23–31–13 hapiotype at least 53,000 years ago, very early in the history of the European population. The number of hapiotype changes seen for two other common mutations, G542X (hapiotype 23–33–13) and N1303K (23– 31–13), suggests that they originated at least 35,000 years ago. Microsateilite allele variability associated with ΔF508, G542X and N1303K demonstrates that slippage and mispairing is the main mechanism generating microsateilite alleles. In spite of the haplotype variability detected for these 3 common mutations, the association between haplotype and mutations is very strong. Mutations 1609delCA, 3667del4, Δ1507 and G551D are all associated with haplotype 16–7–17, which has a frequency of 14.5% in normal chromosomes. 5 haplotypes bearing specific CF mutations were not found in normal chromosomes. Haplotype 16–46–13 is strongly associated with CF mutations E92K and 3601–111G–C. About 23% of CF chromosomes with unknown mutations show significant linkage disequilibrium for microsateilite haplotypes. The strong association between haplotypes and mutations allows the development of frameworks of practical use in diagnosis and in the identification of as yet unknown mutations.