HLA class I and class II loci in Pacific/Asian populations

PCR/SSOP typing was used to identify class I and II alleles in individuals from Malay, Filipino and Papua New Guinea (PNG) Highland populations, as well as two PNG Lowland and three Indonesian populations. Allele frequency distributions were analyzed via population genetic and phylogenetic methods. Three common Australian alleles (DRB1*0405, *0410 and *1407) were seen in the Highlands, and are rare or absent in the other populations. Phylogenetic analyses of DRB1, DPB1 and A allele frequency data indicate a close relationship between the Highlands and Australia. Three putatively new alleles in the HLA-B15 and B56 serogroups were identified in the Highlands (f = 0.01 - 0.05). Variation in homozygosity at the DRB1, DPB1 and A loci suggests that founder effects and positive selection have played significant roles in the history of these populations. A*2402 comprised 78% of the Highlands A-locus alleles, suggesting founder effects, or positive selection for this allele. However, the DRB1, DPB1 and HLA-B loci display no evidence of founder effects in this population, indicating strong directional selection for this allele.