Elucidation of exon 1, 4, and 5 sequences of 39 infrequent HLA-B alleles.

More than 590 human leukocyte antigen (HLA)-B alleles have been identified by sequence analysis. Although the polymorphic exon 2 and 3 sequences of all HLA-B alleles are described, the sequences of the other exons of a number of infrequent B-alleles are unknown. In this study, the exon 1, 4, and 5 sequences of 39 different HLA-B alleles were elucidated by allele-specific sequencing. Overall, these exon sequences showed identity with the majority of the known sequences from the corresponding allele groups, except for four alleles B4010, B4415, B4416, and B5606. The exon 1 sequence of B4010 had nucleotide differences with all B40 alleles, but was identical to the B54, 55, 56, and 59 allele groups. B4416 differed from B440201 at position 988, which was previously considered a conserved position. B4415 showed exon 1, 4, and 5 sequences deviating from the other B44 alleles, but identical to B4501. The exon 1 and 4 sequences of B5606 differed from other B56 alleles, but were in complete agreement with B7801. The deviating exon sequences of B4415 and B5606 confirmed the evolutionary origin of these alleles suggested by the sequences of exons 2 and 3. The polymorphism observed in exons 1, 4, and 5 merely reflects the lineage-specificity of HLA-B.