New DR5 sequences: a novel DRB1*11122 allele identified in Paiwan tribe members of Taiwan and a corrected sequence for the DRB1*1201 allele.

We report herein the identification of a new DRB1 allele using sequence-based typing (SBT). This novel allele, HLA-DRB1*11122, was found in an aboriginal individual (SWP71) from the Paiwan tribe in the southern part of Taiwan. This individual was typed by SBT method as having an HLA genotype of HLA-A*24021/24021, HLA-B*4001/4002, HLA-DRB1*11122/15011, HLA-DRB3*0202, and HLA-DRB5*01011. This new allele differs from DRB1*1112 in the polymorphic exon 2 only at codon 34 (CAA-->CAG; both specify glutamine) and from DRB1*1110 in the exon 2 sequence only at codon 32 (CAT-->TAT; H32T). The most likely candidate allele which is found in the aboriginal populations of Taiwan and which may mutate into this new allele is DRB1*11011. DRB1*11122 allele differs from DRB1*11011 allele in the polymorphic exon 2 at both codon 34 (CAA-->CAG) and codon 37 (TAC-->TTC; T37F). This novel HLA-DRB1*11122 allele was also found in another aboriginal individual (SWP90) from the same Paiwan tribe. This SWP90 individual was typed by SBT method as having an HLA genotype of HLA-A*24021/24021, HLA-B*4002/5502, HLA-DRB1*11122/1201, and HLA-DRB3*01011/0202. However, the original DRB1*1201 sequence from HERLUFF was found to be erroneously reported and the corrected sequence from SWP90 is now presented herein.

Polymorphism of human HLA-DRB1 antigens generated by genetic exchange between DR2 (DRB1*15011) and DR6 (DRB1*1405) alleles: a novel DRB1 allele (DRB1*1437) identified in a Paiwan tribe member of Taiwan.

We report herein the identification of a new DRB1 allele using sequence-based typing (SBT). This novel allele, HLA-DRB1*1437, was found in an aboriginal individual from the Paiwan tribe in the southern part of Taiwan. This individual was typed by SBT method as having an HLA genotype of HLA-A*02011/0203, HLA-B*15011/3901, HLA-DRB1*11011/1437, HLA-DRB3*0202/0202, and HLA-DPB1*0501/1301. This new allele differs from DRB1*1309 in the 5'-end nucleotide sequence of polymorphic exon 2 at codon 16 (CAT-->CAA; H16Q), codon 37 (AAC-->TTC; R37F), codon 47 (TTC-->TAC; F47Y), and codon 58 (GCC-->GCT; both specify alanine). By sequence comparison, it was found that this new allele has a 5'-end sequence (from amino acid residues 7 to 66) identical to that found in the DRB1*1405 allele and a 3'-end sequence (from amino acid residues 58 to 94) identical to that found in the DRB1*15011 allele. Both DRB1*1405 and DRB1*15011 alleles have been identified among the Paiwan members (Note).

Sequence-based typing of HLA class I alleles in Alaskan Yupik Eskimo.

In comparison to South America, native North Americans tend to be less diverse in their repertoire of HLA class I alleles. Based upon this observation, we hypothesized that the Yupik Eskimo would exhibit a limited number of previously identified class I HLA alleles. To test this hypothesis, sequence-based typing was performed at the HLA-A, -B and -C loci for 99 Central Yupik individuals from southwestern Alaska. Two new class I alleles, A*2423 and Cw*0806, were identified. While A*2423 was observed in only one sample, Cw*0806 was present in 26 of the 99 individuals and all of the Cw*0806 samples contained B*4801. Allele Cw*0806 differs from Cw*0803 by a single nucleotide substitution such that Cw*0803 may be the progenitor of Cw*0806. Allele Cw*0803 was originally characterized as unique to South America, but detection of Cw*0803 in the Yupik indicates that Cw*0803 was a founding allele of the Americas. The presence of new alleles and previously unrecognized founding alleles in the Yupik population show that natives of North America are more diverse than previously envisioned.

Class I MHC expression in the yellow baboon.

MHC class I molecules play a crucial role in the immune response to pathogens and vaccines and in self/non-self recognition. Therefore, characterization of MHC class I gene expression of Papio subspecies is a prerequisite for studies of immunology and transplantation in the baboon (papio hamadryas). To elucidate MHC class I expression and variation within Papio subspecies and to further investigate the evolution of A and B loci in Old World primates, we have characterized the expressed class I repertoire of the yellow baboon (Papio hamadryas cynocephalus) by cDNA library screening. A total of nine distinct MHC class I cDNAs were isolated from a spleen cDNA library. The four A alleles and four B alleles obtained represent four distinct loci indicating that a duplication of the A and B loci has taken place in the lineage leading to these Old World primates. No HLA--C homologue/orthologue was found. In addition a single, nonclassical homologue of HLA--E was characterized. Examination of nucleotide and extrapolated protein sequences indicates that alleles at the two B loci are much more diversified than the alleles at the A loci. One of the A loci in particular appears to display very limited polymorphism in both Papio hamadryas cynocephalus and Papio hamadryas anubis subspecies. The failure to detect a homologue of HLA--C in the baboon provides additional evidence for the more recent origin of this locus in the pongidae and hominidae: Further comparative analysis with MHC sequences among the primate species reveals specific patterns of divergence and conservation within class I molecules of the yellow baboon.

Non-conservative substitutions distinguish previously uncharacterized HLA-A molecules.

The extent of class I HLA polymorphism is not yet realized, and to provide a glimpse of the HLA-A polymorphism which remains undetected, we have analyzed approximately 3,700 National Marrow Donor Program (NMDP) Donor/Recipient Pair Retrospective Study Samples with HLA-A DNA sequence-based typing (SBT). Seventeen new HLA-A alleles were detected, with a total of 19 nucleotide substitutions distinguishing these new alleles from their closest HLA-A relatives. Nearly all of the new alleles differ by single nucleotide substitutions; a majority of these substitutions can be explained by gene conversion events but 6 alleles likely originated by point mutation. Fifteen of the 19 nucleotide substitutions translate into amino acid differences in the molecule. Structurally, the inferred amino acid alterations were non-conservative in terms of chemical property, and most substitutions were positioned in 1 or more of the specificity pockets which determine peptide binding. Although these new alleles were identified in a primarily Caucasian sample population, 9 of the 17 new HLA-A alleles were found in samples of non-Caucasoid origin. A new allele detection rate of 1 in approximately 200 individuals in our data set would, therefore, be higher in a non-Caucasoid sample population. In summary, the single nucleotide substitutions that distinguish undetected HLA-A alleles translate into functionally distinct HLA-A molecules. Further studies of the role of HLA-A in transplantation, in disease association, and in evolution must therefore accommodate the discovery of new alleles differing by single nucleotides.

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.