The association between HLA-A, -B alleles and major histocompatibility complex class I polymorphic Alu insertions in four populations in China.

The study of the association between polymorphic Alu insertions [human leukocyte antigen (HLA)-Alu] at five loci and HLA class I alleles at two loci allows for better identification of the origins and evolution of HLA class I region haplotypes in different populations. In the present study, we determined the frequencies of five HLA-Alus and their associations with HLA-A and -B alleles in Han, Wa, Maonan, and Jinuo populations. Our results showed a strong association between AluHG insertion and HLA-A02 in all populations studied; however, the associations between AluHJ insertion and HLA-A1101 and HLA-A2402 and AluHF insertion and HLA-A2601 were only observed in Han. The AluMICB insertion showed a strong association with HLA-B5502 in Han, Maonan, and Jinuo. HLA-A0101, HLA-A0201, HLA-A0203, HLA-A1101, HLA-A2402, HLA-A2601, and HLA-A3101 alleles were associated with one or more of the three different Alu elements within the alpha block as independent haplotypes, and HLA-A0101, HLA-A0201, HLA-A0203, HLA-A1101, and HLA-A*2402 alleles were associated with at least two different Alu insertions as a haplotype within the alpha block. We conclude that the HLA class I region haplotypes of the four populations were derived from different progenitor haplotypes, and relatively high rates of recombination between individuals with HLA-A alleles and different HLA-Alus occurred in this region.