HLA class-I and class-II allele frequencies and two-locus haplotypes in Melanesians of Vanuatu and New Caledonia.

HLA class-I and class-II allele frequencies and two-locus haplotypes were examined in 367 unrelated Melanesians living on the islands of Vanuatu and New Caledonia. Diversity at all HLA class-I and class-II loci was relatively limited. In class-I loci, three HLA-A allelic groups (HLA-A24, HLA-A34 and HLA-A11), seven HLA-B alleles or allelic groups (HLA-B1506, HLA-B5602, HLA-B13, HLA-B5601, HLA-B4001, HLA-B4002 and HLA-B2704) and four HLA-C alleles or allelic groups (HLA-Cw04, HLA-Cw01, HLA-Cw0702 and HLA-Cw15) constituted more than 90% of the alleles observed. In the class-II loci, four HLA-DRB1 alleles (HLA-DRB115, HLA-DRB111, HLA-DRB104 and HLA-DRB116), three HLA-DRB3-5 alleles (HLA-DRB302, HLA-DRB401 and HLA-DRB501/02) and five HLA-DQB1 alleles (HLA-DQB10301, HLA-DQB104, HLA-DQB105, HLA-DQB10601 and HLA-DQB10602) constituted over 93, 97 and 98% of the alleles observed, respectively. Homozygosity showed significant departures from expected levels for neutrality based on allele frequency (i.e. excess diversity) at the HLA-B, HLA-Cw, HLA-DQB1 and HLA-DRB3/5 loci on some islands. The locus with the strongest departure from neutrality was HLA-DQB1, homozygosity being significantly lower than expected on all islands except New Caledonia. No consistent pattern was demonstrated for any HLA locus in relation to malaria endemicity.