Sequence-based typing provides a new look at HLA-C diversity.

Although extensive HLA-A and HLA-B polymorphism is evident, the true diversity of HLA-C has remained hidden due to poor resolution of HLA-C Ags. To better understand the polymorphic nature of HLA-C molecules, 1823 samples from the National Marrow Donor Program research repository in North America have been typed by DNA sequencing and interpreted in terms of HLA-C diversification. Results show that HLA-Cw*0701 was the most common allele with a frequency of 16%, whereas 28% of the alleles typed as Cw12-18 (serologic blanks). The frequency of homozygotes was 9.8% as compared with previous studies of 18% for sequence-specific primers and 50% for serology. Most startling was the frequency at which new alleles were detected; 19 new HLA-C alleles were detected, representing a rate of approximately 1 in 100 samples typed. These new HLA-C alleles result from 29 nucleotide substitutions of which 4 are silent, such that coding substitutions concentrated about the Ag-binding groove predominate. Polymorphism at the HLA-C locus therefore resembles that at the HLA-A and HLA-B loci more than previously believed, indicating that antigenic stress is driving HLA-C evolution. However, sequence conservation in the alpha-helix of the first domain and a clustering of unique amino acids around the B pocket indicate that HLA-C alleles respond to antigenic pressures differently than HLA-A and HLA-B. Finally, because the samples characterized were predominantly from Caucasians, we hypothesize that HLA-C polymorphism will equal or exceed that of the HLA-A and -B loci as DNA sequence-based typing is extended to include more non-Caucasian individuals.

Nucleotide sequence analysis of HLA-B*1523 and B*8101. Dominant alpha-helical motifs produce complex serologic recognition patterns for the HLA-B"DT" and HLA-B"NM5" antigens.

Assigning a precise serologic specificity to the class I HLA-B"NM5" and HLA-B"DT" molecules has proven difficult, with patterns of serologic cross-reactivity suggesting that NM5 is most like antigens in the B5 CREG and that DT is either B7 or B40 like. To better understand the relationship these antigens share with other HLA-B molecules we determined the nucleotide sequence of the alleles encoding HLA-B"NM5" and HLA-B"DT". Sequencing results show that NM5 shares the most overall sequence homology with the B70 antigens and that differences at the alpha-helical Bw4/Bw6 epitope preclude serologic cross-reactivity between NM5 and the B70 antigens. Accordingly, NM5 has been assigned the name B*1523. The strong serologic impact of helical sequence conservations and variations is reiterated for the class I HLA-B"DT" molecule. Comparative analysis demonstrates that sequence conservations in the first domain's alpha-helix stimulate cross-reactivity between HLA-B"DT" and HLA-B7, whereas epitopes conserved in the second domain's alpha-helix impel cross-reactivity between HLA-B"DT" and HLA-B48. To convey the unique lineage of this hybrid B7/B48 molecule the name HLA-B*8101 has been assigned to HLA-B"DT".