Molecular analysis of human leukocyte antigen class I and class II allele frequencies and haplotype distribution in Pakistani population

Aim: Distribution of HLA class I and II alleles and haplotype was studied in Pakistani population and compared with the data reported for Caucasoid, Africans, Orientals and Arab populations.
Materials and Methods: HLA class I and II polymorphisms in 1000 unrelated Pakistani individuals was studied using sequence-specific primers and polymerase chain reaction and assay
. Results: The most frequent class I alleles observed were AFNx0102, BFNx0135 and CwFNx0107, with frequencies of 19.2, 13.7 and 20%, respectively. Fifteen distinct HLA-DRB1 alleles and eight HLA-DQB1 alleles were recognized. The most frequently observed DRB1 alleles which represented more than 60% of the subjects were DRB1 FNx0103, FNx0107, FNx0111 and FNx0115. The rare DRB1 alleles detected in this study were HLADRB1 FNx0108 and FNx0109, having frequencies of 0.9 and 1.7%, respectively. In addition, at DRB1-DQB1 loci there were 179 different haplotypes and 285 unique genotypes and the most common haplotype was DRB1FNx0115-DQB1FNx0106 which represented 17% of the total DRB1-DQB1 haplotypes. In our population, haplotype AFNx0133-BFNx0158-CwFNx0103 comprised 2.8% of the total class I haplotypes observed. This haplotype was seen only in the oriental populations and has not been reported in the African or European Caucasoid.
Conclusion: Our study showed a close similarity of HLA class I and II alleles with that of European Caucasoid and Orientals. In Pakistani population, two rare loci and three haplotypes were identified, whereas haplotypes characteristic of Caucasians, Africans and Orientals were also found, suggesting an admixture of different races due to migration to and from this region.

Keywords
DQB1, DRB1, human leukocyte antigen polymorphism, human leukocyte antigen, HLA-A, HLA-B, HLA-C, Pakistan, population genetics, sequence-specific oligonucleotide analysis