As all HLA class II genes, the DQ genes show their polymorphic variation mainly in the second exon, which encodes the first extracellular domain of the molecule. PCR-SSOP (Polymerase chain reaction-Sequence specific oligonucleotide probe) techniques were frequently used for HLA-DQA1 and DQB1 typing but certain alleles, DQA1^*0101/0104/0105, ^*0302/0303, ^*0501/0505 and DQB1^*0201/^*0202, which differ from each other in segment other than exon 2, could not be unequivocally assigned.

To overcome this problem, we applied additional PCR-SSP (PCR-Sequence specific primer) method to analyze DQA1 exons 1, 3 and 4 and DQB1 exon 3. And we investigated the distributions and haplotypes of HLA-DRB1, DQA1 and DQB1 alleles in 406 unrelated Korean healthy individuals.

Using this method the indistinguishable alleles of DQA1 and DQB1 in PCR-SSOP were typed definitively. We also found several important associations between DQA1 and DQB1 alleles in the Korean population; DQA1^*0101-DQB1^*0501, DQA1^*0104-DQB1^*0502 or -^*0503, DQA1 ^*0105-DQB1^*0501, DQA1^*0302-DQB1^*0303, DQA1^*0303-DQB1^*0401 or -^*0402, DQA1 ^*0501-DQB1^*0201, DQA1^*0505-DQB1^*0301, and DQA1^*0201-DQB1^*0202. The haplotypes of DRB1-DQA1-DQB1 associated with DQA1^*01, ^*03, ^*05, and DQB1^*02 subtypes were investigated. Several haplotypes associated with these alleles were observed in the Korean population.

Our results can be helpful to find potential unrelated donors for bone marrow registries and study the HLA-associated disease and anthropology at high-resolution allelic level.