HLA-DP polymorphism in the present-day San (Bushmen) and Khoi (Hottentots) using polymerase chain reaction and sequence-specific oligonucleotide typing

HLA-DPA1 and DPB1 polymorphism in four Pacific Islands populations determined by sequencing based typing

Class II HLA-DP antigens are heterodimers comprised of alpha and beta chains coded by HLA-DPA1 and HLA-DPB1 genes. Both genes are polymorphic with substantial variation between different populations world wide. This work describes DPA1 and DPB1 polymorphism in four Pacific Island populations of Cook Islands, Samoa, Tokelau and Tonga, living in New Zealand. Using sequencing based typing four DPA1 alleles and twelve DPB1 alleles were observed in total among the four populations. There are two predominant DPA1 alleles DPA1*01031 and DPA1*02022 and three predominant DPB1 alleles DPB1*02012, DPB1*0401 and DPB1*0501. Fourteen DPA1-DPB1 haplotypes in total are present in these four populations with three predominant haplotypes: DPA1*02022-DPB1*0501, DPA1*01031-DPB1*02012, and DPA1*01031-DPB1*0401. Strong positive and negative disequilibrium was observed for individual DPA1-DPB1 haplotypes. Significant differences in DPA1 and DPB1 allele and haplotype frequencies were observed between Tokelauan and other three populations. Phylogenetic analysis of genetic distances between the four Pacific Island populations and other Asian Oceanian populations have shown that Cook Islanders, Samoans and Tongans are more closely related to Asian populations whereas Tokelauans cluster towards non-Austronesian populations of Papua New Guinea Highlanders and Australian Aborigines.

C4 polymorphism and extended HLA haplotypes in Namibian San and Khoi and in South African Xhosa

We studied C4A and C4B polymorphisms and HLA-B and -DR associations in the San, Khoi and Xhosa. C4A and C4B alleles were determined using conventional protein allotyping methods. The C4A*3, C4B*1 haplotype had a high frequency (30-55%) in all populations. The frequency of C4A*3, C4B*Q0 was 7-19%. The C4A*Q0, C4B*1 haplotype was frequent (15%) in the Khoi but very rare in the San (P < 0.001). C4A*12 A*91, C4B*Q0 was frequent in the Xhosa (15%) but rare in the San and Khoi (P < 0.001). Alleles C4A*5 and C4A*6, and the C4B*2 B*92 duplication were only found in the Xhosa. C4A alleles A*4, A*45, A*58, A*12, A*14, A*19 and the C4A*3 A*91 duplication were only found in the San/Khoi population group. In the San, fourteen extended haplotypes were found in a relatively high frequency (2-7%). In the Xhosa, one extended haplotype (B42, C4A*12 A*91, C4B*Q0, DR18) was found in a very high frequency (13%) and was characteristic for this group; five other extended haplotypes were found with a low frequency (< 3%).

HLA-DPB1 DNA polymorphism in the Swiss population: linkage disequilibrium with other HLA loci and population genetic affinities

Allelic diversity at the HLA-DPB1 locus was determined by PCR-oligotyping in a sample of 125 healthy Swiss individuals. A total of 17 alleles were detected among which four main alleles (DPB1*0401, *0201, *0301, *0402) reached a cumulative frequency of 74.8%. HLA-A and -B (by serology) and HLA-DRB1 (by oligotyping) allelic polymorphisms were analysed also. HLA-B and HLA-DRB1 loci were highly polymorphic with 25 and 28 alleles respectively and similar heterozygosity levels of 0.93 and 0.92. These two loci were found to be more polymorphic than expected under neutrality, while lower heterozygosity levels were found for HLA-A (0.87) and DPB1 (0.81) loci. This paper presents also a global comparison of DPB1 allelic frequencies among 15 populations from four continents. As opposed to the DRB1 locus, overall DPB1 is shown to have a lower level of polymorphism and may be considered as neutral in all tested populations. DPB1 genetic diversity is correlated significantly with geography also, as found previously for DRB1. Two- and four-locus haplotype frequencies were determined and the significance of their linkage disequilibrium tested by an original non-parametric method. A significant positive linkage disequilibrium was found for 11 A-B, 16 B-DRB1, 7 DRB1-DPB1 and 3 A-B-DRB1-DPB1 haplotypes. The overall linkage disequilibrium between DRB1 and DPB1 was much lower than expected from the physical distance and lower than for A-B and B-DRB1 pairs. The implications of these results for bone marrow transplantation and for the evolution of HLA loci are discussed.