The DQA1*0104 allele is carried by DRB1*1001- and DRB1*1401-positive haplotypes in Caucasians, Africans and Orientals.

The DQA10104 allele is known to differ from DQA10101 by a single nucleotide in the sequenced part of the first exon. DQA10104 has a guanine in the second position of the second expressed codon, whereas DQA10101 and all other sequenced DQA1 alleles have an adenine in that position, changing aspartic acid to glycine. The DQA10104 allele was originally described in African Americans with the DRB112, DRB30101, DQA10104, DQB10501, DRB112, DRB30202, DQA10104, DQB10605 or DRB114, DQA10104, DQB10503 haplotypes. When developing DQA1 typing by PCR amplification with sequence-specific primers (PCR-SSP), we observed that all DR10- and DR14-positive samples carried the DQA10104 allele, whereas all DRB101-positive DNAs carried the closely related DQA10101 allele. In the present study, samples representing the major ethnic groups with DR-DQ haplotypes known to carry the DQA10104 allele or the very similar DQA10101 allele were investigated by TaqI RFLP analysis, PCR-SSP typing and nucleotide sequencing. The DQA10104 allele was found to differ from DQA10101 not only in the second expressed codon, but also by a productive mutation in the signal peptide. All investigated DRB11001-(n = 24) and DRB11401-positive (n = 25) haplotypes, defined by homozygosity or association, of Caucasian, African or Oriental origin carried the DQA10104 allele, whereas the DQA10101 allele was found on all DRB101-positive (n = 32) haplotypes. These findings demonstrate that in the assignment of HLA class II alleles, polymorphism outside the second exon sometimes must be considered.(ABSTRACT TRUNCATED AT 250 WORDS)