HLA-A, -B, -C, -DRB1 allele and haplotype frequencies in an African American population

Sequence-based typing was used to identify human leukocyte antigen (HLA)-A, -B, -C, and -DRB1 alleles from 564 consecutively recruited African American volunteers for an unrelated hematopoietic stem cell registry. The number of known alleles identified at each locus was 42 for HLA-A, HLA-B 67, HLA-C 33, and HLA-DRB1 44. Six novel alleles (A*260104, A*7411, Cw*0813, Cw*1608, Cw*1704, and DRB1*130502) not observed in the initial sequence-specific oligonucleotide probe testing were characterized. The action of balancing selection, shaping more 'even' than expected allele frequency distributions, was inferred for all four loci and significantly so for the HLA-A and DRB1 loci. Two-, three-, and four-locus haplotypes were estimated using the expectation maximization algorithm. Comparisons with other populations from Africa and Europe suggest that the degree of European admixture in the African American population described here is lower than that in other African American populations previously reported, although HLA-A:B haplotype frequencies similar to those in previous studies of African American individuals were also noted.

DRB3 alleles with variations in the annealing sites of commonly used amplification primers

New HLA alleles are often identified initially from observing uncommon patterns found in low-resolution typing performed via polymerase chain reaction using sequence-specific oligonucleotide probes (PCR-SSOP). Recently, the HLA-DR oligotyping analysis of two Caucasian, one Caucasian/American Indian and two African American individuals resulted in the identification of three novel DRB3 alleles. Using DRB-specific primer sets commonly employed in amplification-based typing, all four individuals were originally characterized as DRB3 negative. Direct sequencing identified DRB3*0104 (variation at codon 8, TCG instead of TTG), and DRB3*0101202 (variation at intron (-13), G instead of C). One individual appeared to carry a DR52-associated DRB1 allele without an associated DRB3 allele. Lack of conservation at the junction of intron 1 and exon 2 of the DRB3 gene suggests that commonly used DRB-specific primer sets may need to be modified.

Two DR2-associated novel alleles arose from the silent mutation of codon 72: DRB1*16012, DRB5*01012

Two DRB1*02-associated alleles, DRB1*16012 and DRB5*01012, are described. Both alleles carry the same silent substitution at codon 72.

The complexity of DRw6 and DR5 haplotypes in American blacks demonstrated by serology, cellular typing, and restriction fragment length polymorphism analysis

This study describes the diversity of DRw6 and DR5 haplotypes in the American black population using serology, cellular typing, and restriction fragment length polymorphism (RFLP) analysis. DRw6 (DRw13 and DRw14) and DR5 (DRw11 and DRw12) haplotypes are observed at a high frequency in this population (DRw6: 32%, DR5: 30%). Many of these haplotypes express undefined HLA-D specificities and unusual DQ and DRw52 associations which previously have not been well characterized or reported (e.g., DRw13, DQw5, DRw52c, D-; DRw13, DQw2, DRw52a, D-; DRw11, DQw5, DRw52c, D-). Serologic analysis of class II alleles in American blacks suggests the presence of DRw13, DRw11 and DQw6 allelic variants and demonstrates the difficulty in defining DRw6 and DR5 in this population. The class II genes from four American black families expressing many of the novel DRw13, DRw14, DRw11, and DRw12 haplotypes defined by serology and mixed leukocyte culture were further characterized by RFLP analysis. The data presented here along with other published data identify at least eight DRw13 haplotypes (DRw13A-DRw13H) in the human population. Five of these haplotypes exhibit an undefined HLA-D specificity. Three DRw14 haplotypes (DRw14A-DRw14C) and eight DR5 haplotypes (DRw11A-DRw11E and DRw12A-DRw12C) were also identified. The novel DRw6 and DR5 haplotypes observed in American blacks may arise from differences in DRB1, DQA1, and DQB1 genes as well as from differences in the combinations of alleles of these genes encoded by a haplotype. The serologic and RFLP analyses suggest that some DRw13 and DRw11 haplotypes represent transitional steps between DRw13 and DRw11 in the evolutionary pathway which generated the DRw52 family.

The DR3(w18),DQw4 haplotype differs from DR3(w17),DQw2 haplotypes at multiple class II loci

The polymorphism of HLA class II molecules in man is particularly evident when comparisons between population groups are made. This study describes a DR3 haplotype commonly present in the American black population. Unlike the Northern European population, in which almost all DR3 individuals are DQw2, approximately 50% of DR3-positive American blacks express a DQw4 allelic product. This study characterizes the DR subregion of that haplotype. cDNA sequence analysis has revealed a DR beta gene which differs at several positions from previously described DR3 beta 1 genes. It is postulated that a gene-conversion-like event with a DRw52 beta gene as donor has generated some of these differences. The haplotype carries a DRw52a allele as defined by oligonucleotide hybridization studies. DNA restriction fragment analysis using a family and several unrelated individuals has allowed us to identify DR alpha and beta fragments associated with the DR3(w18),DQw4 haplotype. The most striking observation is that the DR3(w18),DQw4 haplotype differs from DR3(w17),DQw2 haplotypes at multiple class II loci. Several genetic mechanisms including reciprocal recombination, gene conversion, and point mutation were involved in generating the differences between these haplotypes. Once established, the DR3(w18),DQw4 haplotype appears to be relatively stable in the population.

Polymorphism of the HLA-DR1 haplotype in American blacks. Identification of a DR1 beta-chain determinant recognized in the mixed lymphocyte reaction

Mixed lymphocyte typing provides an exquisitely sensitive means of detecting the polymorphism of HLA class II molecules. By using this technique, the differences between divergent human populations become apparent. This study describes a DR1 haplotype commonly present in the American black population. Unlike the Northern European population in which almost all DR1 individuals are DQw1 and type as Dw1 by using mixed lymphocyte typing, approximately 50% of DR1, DQw1 positive American blacks express an undefined Dw specificity. The DR beta polypeptide encoded by a DR1,Dw-cell differs from a previously described DR1,Dw1 beta sequence by two amino acid replacements at positions 85 and 86 in the first domain. One silent nucleotide substitution has also been identified. DQ alpha and beta first domain cDNA sequences from this haplotype are identical with previously described DQ sequences from a DR1,Dw1 cell. This relatively minor change in amino acid sequence of the DR molecule appears to produce the undefined HLA-D specificity in this haplotype. The variant DR1 sequence is shared with a DR beta-chain from the DR2,DwMN2 haplotype suggesting that a gene conversion-like mechanism has generated this difference.

Polymorphism of the HLA-DR1 haplotype in American blacks. Identification of a DR1 beta-chain determinant recognized in the mixed lymphocyte reaction

Mixed lymphocyte typing provides an exquisitely sensitive means of detecting the polymorphism of HLA class II molecules. By using this technique, the differences between divergent human populations become apparent. This study describes a DR1 haplotype commonly present in the American black population. Unlike the Northern European population in which almost all DR1 individuals are DQw1 and type as Dw1 by using mixed lymphocyte typing, approximately 50% of DR1, DQw1 positive American blacks express an undefined Dw specificity. The DR beta polypeptide encoded by a DR1,Dw-cell differs from a previously described DR1,Dw1 beta sequence by two amino acid replacements at positions 85 and 86 in the first domain. One silent nucleotide substitution has also been identified. DQ alpha and beta first domain cDNA sequences from this haplotype are identical with previously described DQ sequences from a DR1,Dw1 cell. This relatively minor change in amino acid sequence of the DR molecule appears to produce the undefined HLA-D specificity in this haplotype. The variant DR1 sequence is shared with a DR beta-chain from the DR2,DwMN2 haplotype suggesting that a gene conversion-like mechanism has generated this difference.

Polymorphism of the HLA-D region in American blacks. A DR3 haplotype generated by recombination

The polymorphism of HLA class II molecules in man is particularly evident when comparisons between population groups are made. This study describes a DR3 haplotype commonly present in the American black population. Unlike the Northern European population in which almost all DR3 individuals are DQw2, approximately 50% of DR3-positive American blacks express a serologically undefined DQ allelic product. DNA restriction fragment analysis with the use of several unrelated individuals and an informative family has allowed us to identify unique DQ alpha- and beta-fragments associated with the DR3, DQw- haplotype. Based on fragment size, the DQ alpha genes of the DR3, DQw- and DRw8, DQw- haplotypes are similar as are the DQ beta genes of DR3, DQw-; DRw8, DQw-; and DR4, DQw- haplotypes. In addition, a DX beta gene polymorphism has been identified which is associated with some DR3 haplotypes including the American black DR3, DQw- haplotype. cDNA sequence analysis has revealed a DQw2-like alpha gene and a DQ beta gene which is similar to that previously described for a DR4, DQw- haplotype. It is postulated that recombination between DQ alpha and DQ beta genes and between the DQ and DX subregions has generated the various DR3 haplotypes and has played an important role in creating diversity in the HLA-D region.

Polymorphism of the HLA-D region in American blacks. A DR3 haplotype generated by recombination

The polymorphism of HLA class II molecules in man is particularly evident when comparisons between population groups are made. This study describes a DR3 haplotype commonly present in the American black population. Unlike the Northern European population in which almost all DR3 individuals are DQw2, approximately 50% of DR3-positive American blacks express a serologically undefined DQ allelic product. DNA restriction fragment analysis with the use of several unrelated individuals and an informative family has allowed us to identify unique DQ alpha- and beta-fragments associated with the DR3, DQw- haplotype. Based on fragment size, the DQ alpha genes of the DR3, DQw- and DRw8, DQw- haplotypes are similar as are the DQ beta genes of DR3, DQw-; DRw8, DQw-; and DR4, DQw- haplotypes. In addition, a DX beta gene polymorphism has been identified which is associated with some DR3 haplotypes including the American black DR3, DQw- haplotype. cDNA sequence analysis has revealed a DQw2-like alpha gene and a DQ beta gene which is similar to that previously described for a DR4, DQw- haplotype. It is postulated that recombination between DQ alpha and DQ beta genes and between the DQ and DX subregions has generated the various DR3 haplotypes and has played an important role in creating diversity in the HLA-D region.

The HLA-DP polymorphism in Denmark investigated by local and international PLT reagents. Definition of two "new" DP antigens

Lymphocytes from highly selected donors were primed for 10 days and subsequently bulk-expanded in IL 2 (TCGF) containing cultures. Two well-discriminatory PLT (CDP = Copenhagen DP) reagents against each of the DPw1-w6 specificities and one against each of the two "new" specificities, CDP4s and CDPHEI, were selected for further studies. Three combinations made in two recombinant families and four of ten HLA-A, B, and DR compatible combinations discriminated well in contrast to seven of 46 DR compatible, but HLA-A or B incompatible combinations. All reagents gave highly reproducible results, and high correlations (r-values between 0.73-1.00) for DP assignments were obtained with CDP and GNN reagents. No triplets were found for the DPw1-w6 and CDP HEI specificities. The "new" specificity CDP HEI defined in an HLA-DR/GLO recombinant family gave a coefficient of correlation with GNN 8 of 0.91. Another "new" specificity, CDP4s constitutes a subgroup ("split") of DPw4. The gene frequencies of DPw1-w6 estimated in 102 unrelated randomly selected Danes agreed with those reported for other Caucasoid populations. The gene frequencies CDP HEI and CDP4s were 0.03 and 0.08, respectively. The associations between DR3-DPw1, DR2-DPw4, and DRw6-DPw2 were confirmed. It is concluded that DP-typing with bulk-expanded reagents is a reliable and so far the only technique which can reveal the polymorphism of the DP gene products.

An HLA-DR/DP recombinant family involving DPw6. Evidence for cross-reactivity between DPw6 and GNN2B

HLA typing of an HLA-B/GLO recombinant family using bulk-expanded DP(SB) alloreactive T-cells (GNN1 to 6) as well as conventional HLA-ABC, D, DR, and DQ typing showed that a paternal recombination had taken place between HLA-DR and DQ on the one hand and HLA-DP(SB) on the other. The recombinant child was DPw4,6-heterozygous and differed in terms of class II determinants only for DPw6 from two otherwise HLA identical siblings, who were probably DPw4/4-homozygous. These siblings did not stimulate the recombinant in MLC whereas they responded to his cells indicating that DPw6 can stimulate in primary MLC. Moreover, it was possible to generate and bulk-expand DPw6-reactive lymphocytes (PLs) between MT and MA as responders and BN as stimulator. The correlation coefficient (r) between the reaction of these PLs and the GNN6 (anti-DPw6) reagents was 1.0 when tested against a panel of 71 individuals. This is the first report demonstrating that the DPw6 gene, like the DPw1-w5 genes, is located between DR/DQ and GLO. The frequency of the DPw6 antigen in 41 unrelated, randomly selected Danes was 7%. HLA-DP typing of the BN family revealed that the DPw6 positive but not DPw6 negative family members gave intermediate responses with one (GNN2B) but not with another (GNN2A) anti-DPw2-reagent. Studies of 63 healthy individuals (unrelated to the BN family) revealed seven similar discrepancies between GNN2A and GNN2B. Strikingly, all four DPw6 positive stimulators gave rise to such discrepancies indicating that the GNN2B reagent is cross-reactive and recognize a common part of the DPw2 and DPw6 molecules. No cases of GNN2A+/GNN2B- stimulators were found.

Complotype genetic loci segregate more frequently with HLA-DR than with HLA-B

The loci for BF, C2, C4A, and C4B are very closely linked to each other so that alleles of these plasma protein markers occur in populations in linkage disequilibrium and are inherited as single genetic units called complotypes. These complotypes are coded by a DNA region of the short arm of chromosome 6 embracing approximately 100 kilobases, which serve as a marker of the major histocompatibility complex. We have studied the complotypes of nine families with known HLA-B/DR crossovers. In seven families, the complotypes were inherited with HLA-DR, including in one family with a double recombination. The haplotype HLA-A28, Cw1, B27, FC3, 20, DR4 of JTr resulted from two recombinations between HLA-A2, Cw1, B27, SC42, DR7 and HLA-A28, Cwx or Cw1, B37, FC3, 20, DR4. In the remaining two families (Ro and Lo) the complotypes were inherited with HLA-B. The haplotype A2, Cw5, Bw44, SC30, DR3 of StLo resulted from paternal recombination between the haplotypes A2, Cw5, Bw44, SC30, DR4 and A24, B8, SC01, DR3, and the haplotype A24, Cw4, Bw35, SC31, DR3 of NaRo resulted from maternal recombination between A24, Cw4, Bw35, SC31, DR4 and A26, Bw41, FC31, DR3. Our data suggest that the complotype region maps closer to HLA-D than to HLA-B.

Selective production of human antigen specific helper factor from normal volunteers: implications for human Ir genes

Based on previous systems for generating helper cells and factors from mouse spleen cell cultures, an in vitro system for the production and detection of human helper factors to the synthetic polypeptide antigens (T,G)-A--L and GAT10 was developed. The factors are made by human peripheral blood leucocytes and are antigen-specific, as judged both by functional criteria and specific binding and elution from antigen columns. Out of the first six volunteers studied two were high responders to (T,G)-A--L, but non-responders to GAT, two responders to GAT but not (T,G)-A--L. One subject made factors to both antigens and the sixth reacted to neither. The antigens chosen are known to be under MHC-linked immune response (Ir) gene control in all animal species tested, with some strains being responders while others are not. The selective responsiveness, different between individuals, thus suggests that the response to these antigens in man is under Ir gene control. Because of the small size of the sample initially studied and HLA typed, it was not surprising that there was no clear-cut association of response with any particular histocompatibility type at the HLA-A, B, C or D locus.