The sequence and characterisation of ?-globin haplotypes in human populations

Genetic variation at the human a-globin gene complex has only been characterised to date as haplotypes - a linked set of 7 RFLPs and 2 VNTRs - and not at the sequence level. However, an understanding of the extent of sequence variability at this locus, and its relation to underlying mutational processes, is of interest to studies of both molecular and population genetics. This variation has been investigated by the development of a PCR haplotyping and direct sequencing protocol. Sequencing of 6 RFLP-containing regions of the haplotype in different human populations demonstrates that all (-) RFLPs have the same sequence, regardless of geographical origin. Additional sequence variation is found surrounding the RFLP sites, indicating that the overall level of variation at this locus is comparable to that at other loci, although a higher mutation rate is shown in an inter-species comparison. The additional polymorphic sites are concentrated in only three regions; a survey comprising a total ~280kb indicates that this sequence polymorphism is generated and influenced by localised gene conversion, which was not evident at the RFLP level. PCR analysis of the 2 VNTRs in human populations demonstrates considerable size variation in human populations, not detected by previous haplotyping protocols. There is also extensive internal sequence variation in the VNTRs (in a total survey of ~50 kb), apparently accumulating in a polar fashion and governed primarily by gene conversion, as reported at other VNTR loci. In addition, flanking sequence variation is identified which undergoes conversion, although not in concert with changes in the nearby repeat structure. Consideration of the association of variation, at both the unique and repeated sequence regions, with RFLP α-haplotypes demonstrates that haplotypes differ in age, and allows relationships between them to be determined. The resulting haplotype network has similarities to that determined from β-globin gene variation; the implications for recent human evolution are discussed.