Worldwide genetic analysis of the CFTR region

Abstract

Mutations at the cystic fibrosis transmembrane conductance regulator gene (CFTR) cause cystic fibrosis, the most prevalent severe genetic disorder in individuals of European descent. We have analyzed normal allele and haplotype variation at four short tandem repeat polymorphisms (STRPs) and two single-nucleotide polymorphisms (SNPs) in CFTR in 18 worldwide population samples, comprising a total of 1,944 chromosomes. The rooted phylogeny of the SNP haplotypes was established by typing ape samples. STRP variation within SNP haplotype backgrounds was highest in most ancestral haplotypes-although, when STRP allele sizes were taken into account, differences among haplotypes became smaller. Haplotype background determines STRP diversity to a greater extent than populations do, which indicates that haplotype backgrounds are older than populations. Heterogeneity among STRPs can be understood as the outcome of differences in mutation rate and pattern. STRP sites had higher heterozygosities in Africans, although, when whole haplotypes were considered, no significant differences remained. Linkage disequilibrium (LD) shows a complex pattern not easily related to physical distance. The analysis of the fraction of possible different haplotypes not found may circumvent some of the methodological difficulties of LD measure. LD analysis showed a positive correlation with locus polymorphism, which could partly explain the unusual pattern of similar LD between Africans and non-Africans. The low values found in non-Africans may imply that the size of the modern human population that emerged "Out of Africa" may be larger than what previous LD studies suggested.

Figure 1

CFTR gene with all six polymorphic genetic markers studied (IVS1CA, IVS6aGATT, IVS8CA, T854, IVS17bTA, TUB20), showing the physical distances (in kb) between them. Gene exons are denoted by numbers (1–24).

Figure 2

LD D′/ξ values correlation between loci IVS6aGATT / T854 and T854 / TUB20 (significance level for D′, P<.05)

Figure 3

ξ values for four populations between all six loci (1=IVS1CA, 2=IVS6aGATT, 3=IVS8CA, 4=T854, 5=IVS17bTA, and 6=TUB20). Each square is a graphical representation of ξ levels for pairs of loci in two populations; each population is represented either above or below the diagonal (gray squares).