A novel recombinant HLA-B*39 allele (B*3910) in a South African Zulu

The sequence of a new B*39 allele has been identified in a South African Zulu individual. This allele, designated B*3910, differs at two nucleotide positions (246 and 272) from B*39011. The difference at position 246 is silent, while that at position 272 results in an amino acid change from cysteine (B*39011) to tyrosine (B*3910). As these same differences are found in other HLA-B alleles, they were probably introduced into the B*3910 sequence by a short gene conversion event with another allele. This finding provides further evidence for the diversification of HLA-B allelic sequences via recombination.     

Characterization a novel HLA-B40 allele with serological Bw4 motif, HLA-B*4047, in the Finnish population and confirmation of B*270503 allele

We describe a novel HLA-B*40 allele assigned as B*4047*. The B*4047 allele was detected in a Finnish patient awaiting kidney transplantation. The patient had a "short" B60-like serological specificity with Bw4 association. After sequencing, the B*4047 allele was found to be identical to B*4001, except having five amino acid changes in exon 2, including the entire motif corresponding to Bw4 and w6 specificity. As a result of recombination or gene conversion, B*4047 has the Bw4 motif instead of expected Bw6. Screening of B40 alleles in the Finnish population revealed no other cases with this pattern, suggesting that this allele is rare. The sequence of B*270503 presented here provides the complete sequence for exons 2 and 3 for this allele. B*270503 allele differs from B*270502 by a single synonymous nucleotide substitution at non-variable position 489 in exon 3.     

Immunogenetic study of a new HLA allele,B*2723

A novel HLA-B*27 allele (B*2723) detected by irregular serological and PCR-SSP typing results was identified by nucleotide sequencing of exons 2 and 3. B*2723 differs from B*27052 by nine nucleotides which encode seven amino acid changes at positions 63 (Glu to Asn), 67 (Cys to Phe), 69 (Ala to Thr), 70 (Lys to Asn), 71 (Ala to Thr), 74 (Asp to Tyr) and 77 (Asp to Ser) in the alpha1 helix. All these substitutions are possessed by B*35 alleles suggesting that B*2723 was created by a gene conversion-like event involving B*27052 and a B*35 allele. Using the HLA-A*26 and DRB1*12 alleles of the B*2723-bearing haplotype as 'markers', two further examples of B*2723 were found in 29,851 blood donors. Therefore, B*2723 has a 'minimum' gene frequency of 0.000034 (phenotype frequency 0.0067%) in blood donors resident in Wales. In all three families, B*2723 was present on a haplotype with: A*26; Cw*0202; DRB1*1201/6/7; DRB3*02; DQA1*05; DQB1*0301. The B*2723 product failed to react with HLA-B27 antisera and reacted weakly or not at all with Bw4 antisera. Lack of the ECAKA motif at amino acid positions 63, 67, 69-71 probably accounts for lack of the B27 specificity while the amino acid combination 74Y, 77S, 80T, 81L may cause aberrant Bw4 reactivity.     

HLA-B67: A member of the HLA-B16 family that expresses the ME1 epitope

Abstract: HLA-B67 is an uncommon antigen that has been defined by serological crossreactivity with the HLA-B7 and HLA-B16 (B38 and B39) antigens. It is found at highest frequency in certain Oriental populations and has been best defined in the Japanese. Nucleotide sequencing of cDNA encoding B67 reveals the B*6701 allele to be a subtype of B39 which differs from B*39011 by substitution at residues 67–71 of the α₁ helix. In the region of difference B*6701 is identical in sequence to B7, B22, B27 and related molecules that express the epitope recognized by the ME1 monoclonal antibody. That the HLA-B67 molecule binds strongly to the ME1 antibody was demonstrated by immunoprecipitation and cell surface binding assays. Identical B*6701 nucleotide sequences were obtained for the B67 alleles isolated from 2 unrelated Japanese and 1 North American caucasoid.     

Novel HLA allele, HLA-B*4013, identified from a potential bone marrow recipient. Putative gene conversion events with donor sequence

A new B40 allele was identified in a leukemic Caucasian patient. This allele, designated B*4013, differs in alpha 1 domain from B*4002 at six amino acidic positions: 67, 77, 80, 81, 82 and 83. Most of this substitutions could alter the antigen binding site of the HLA-B molecule. B*4013 may have originated by gene conversion or reciprocal recombination involving B*4002 as the recipient allele of sequence donated by B*4406. The new allele was serologically typed as a "blank" associated with the Bw4 epitope.     

Unexpected Bw4 and Bw6 reactivity patterns in new alleles

The Bw4 and Bw6 epitopes were the first HLA-B differences to be recognized by serological methods. Since then 44 serological groups have been identified and more than 250 alleles assigned by molecular typing methods. In general each serological HLA-B group is associated with the presence of either the Bw4 or the Bw6 epitope. There are several exceptions to this rule. Four alleles, B*4601, *7301, *5503 and *1806, show no serological reactivity with either Bw4 or Bw6. Although the Bw6 motif at residues 77-83 is present in these alleles the Bw6 epitope is modified by a valine at residue 76. One or more alleles from the B8, B40 and B62 groups are identified as Bw4 positive, whereas all others are Bw6 positive. In the groups B27, B44 and B47 several alleles are found to be Bw6 positive, while the majority is Bw4 positive. Histocompatibility testing of dialysis patients and their families revealed the serological presence of an unexpected Bw4 epitope associated with B18 in one patient and B56 in another. Allele-specific amplification and sequencing of exons 2 and 3 of these HLA-B alleles revealed the presence of the Bw4 sequence motif for both. The new alleles were assigned B*1809 and B*5607, respectively. In 2 other patients the presence of a new B*07 allele was determined by sequence based typing. Although the new allele, B*0715, showed the Bw6 sequence motif at positions 77 to 83, a substitution of amino acid 76 from glutamic acid to valine was identified. This change resulted in an aberrant Bw6 serological reaction pattern.     

Additional diversity within the B70 serotype: identification of B*1580 in a Caucasoid blood donor

Anew B70 variant, B*1580, has been identified in a Swiss Caucasoid blood donor. Sequencing of exons 2 and 3 revealed that the HLA-B*1580 differs from its closest matching allele B*1518 by two substitutions in exon 3, leading to two amino acid changes, threonine to isoleucine and leucine to isoleucine at codons 94 and 95, respectively. The complete human leukocyte antigen type of the donor is: A*2402, A*2601; B*5101, B*1580; Cw*0704, Cw*1402/05; DRB1*0801, DQB1*0402. The B*1580 is a new member of the B70 cluster, characterized by the SEE motif at positions 24, 45, and 46 in the alpha1-domain. Substitutions at codons 94 and 95, also found in some B62 and B75 alleles, do not appear to interfere with the B70 serological reactivity. Based on sequence similarity and linkage with Cw*0704, the rare alleles B*1509, B*1529, B*1564, and B*1580 are possibly derived from the B*1518 haplotype.     

Structural definition of the A*74 group: implications for matching in bone marrow transplantation with alternative donors

We have identified two new A*74 alleles (A*7402 and 7403) in two unrelated individuals. A*7402 differs from A*7401 by a single amino acid substitution in the signal peptide and may be the result of a gene conversion event at the 3' end of exon 1. A*7403 differs from A*7401 by a single amino acid exchange in the α1 domain and is most likely due to a point mutation in exon 2, since no HLA class I donor allele has been found. Since A*7402 appears to be the ancestor of the other two A*74 alleles, it is possible that A*7401 and 7403 have been created by successive point mutations. The sequences of the expressed proteins of A*7401 and 7402 are identical. The heavy chain sequence of A*7403 differs from these alleles at the crucial residue 79 which is located in the sequence stretch of the al α-Helix where the Bw4/Bw6 determinants have been identified and which probably affects TCR interaction. This variation can therefore be expected to stimulate alloreactive T cells, graft rejection and graft versus host disease emphasizing the relevance for matching in bone marrow transplantation with alternative donors.     

New alleles in the B44 family including B*44022, B*44032, B*4411, B*4420, B*4421, B*4424, and B*8301

Seven new HLA-B locus alleles have been described. B*44022 and B*44032 are silent substitutions altering known alleles. B*4411 carries a unique Bw4-like epitope. B*4420, B*4421, and B*4424 carry new combinations of motifs previously observed in other alleles. B*8301 appears to be the result of the replacement of exon 2 from B*4402 with exon 2 from B*5603.     

Identification of two new HLA-B22 variants, HLA-B*5509 and B*5606

In our recent study using high-resolution HLA-B locus typing by sequence-based typing (SBT) we identified 9 new alleles in a total of 355 unrelated individuals (4). Three of them concerned an allele belonging to the B22 group. One of them, B*5607, showed the unusual presence of a Bw4 sequence motif, as described previously (5). In this report the other two B22 variants are described; one belonging to the B55 specificity and named B*5509; the other one being a B*56 allele and assigned B*5606, which brings the total number of alleles belonging to the B22 group to 18.     

Sequence-based typing of exons 1-5 of a new HLA-B allele, B*3927*

Anew human leucocyte antigen-B (HLA-B) allele, B*3927, was detected in three individuals of a Caucasian family by routine typing with sequence-specific primers (SSP). Serological typing showed B27 Bw4 and B39 Bw6, whereas SSP detected only B*27 as well as the Bw4 and Bw6 motif. The sequence of exons 1-5 of the new allele was determined by allele-specific amplification and sequencing. The new B*39 allele showed one nucleotide difference with B*390101 at position 299 in exon 2. Codon 100 changed from GAG to GTG, resulting in an amino acid substitution from glutamic acid to valine at position 76 of the mature protein. The haplotype carrying the B*3927 allele was A*010101, B*3927, Cw*120301, DRB1*0101 and DQB1*050101.     

Detection of a novel HLA‐B27 allele,B*2740, in Taiwanese volunteer bone marrow donors by sequence‐based typing: curiosity rewarded

We report here a novel HLA‐B allele, B*2740, discovered in Taiwanese volunteer marrow donors. The new sequence has nucleotide variation at position 527 (T→A) as compared to B*2708. The nucleotide change caused an amino acid substitution from valine (V) to glutamic acid (E) at codon 152. Since B*2740 carries sequence confers to HLA‐Bw6 public epitope we believe that this novel B*27 allele might have been generated from a gene conversion involving a Bw4‐specific allele (probably B*2704) and a Bw6‐specific allele.     

Novel HLA-B alleles, B*8201, B*3515 and B*5106, add to the complexity of serologic identification of HLA types

Three class I alleles, B*8201, B*3515 and B*5106, have been described using DNA and cDNA sequencing. The B*8201 allele is most structurally related to B*5602, differing from it by 14 nucleotide substitutions resulting in 5 amino acid differences. The other two alleles, B*3515 and B*5106, differ from their most closely related HLA-B alleles by 2–3 nucleotide substitutions resulting in 1–2 amino acid substitutions, respectively. The majority of nucleotide substitutions marking these new alleles are observed in other HLA-B alleles suggesting that gene conversion and/or reciprocal recombination have created this diversity. All of the amino acid substitutions are predicted to alter the antigen binding site of the HLA-B molecule. The newly defined HLA-B allelic products were originally defined by their unusual serologic reactivity patterns. The B*8201 allelic product is serologically typed as a B "blank" or as a variant of B22 or B45. These patterns and the serologic reactivity of the other newly described allelic products are consistent with the protein sequence homology among specific HLA-B molecules. While serology remains a powerful tool for detecting HLA diversity, alleles generated by events resulting in the sharing of HLA sequence polymorphisms among alleles at a locus will continue to create complexity in the interpretation of typing results.     

A novel B*38 allele, B*3809, was identified via sequence -based typing of B-cell line no. 299 of the UCLA International Cell Exchange

In this paper we report the identification of a new HLA-B allele in a sample that was distributed in the International UCLA Terasaki Cell/DNA Exchange, and the results were summarized in the final report of the 280th Cell Exchange. This novel allele officially designed B*3809 was found in B-cell line no. 299 from a Dutch Caucasoid donor and differs from B*3801 by mutation C-->G at position 483 in exon 3, resulting in an amino-acid substitution at codon 161 from aspartic acid in B*3801 to glutamic acid in B*3809, respectively.     

Immunogenetics of two new HLA-B alleles: B*4414 and B*5708

Two new alleles, HLA-B*4414 and B*5708, were identified in north-western European Caucasoid blood donors. B*4414 differed from B*440201 by two nucleotide substitutions in exon 3 [positions 66 (T to C) and 69 (G to A)] producing two amino acid differences between the B*440201 and B*4414 specificities (tyrosine to histidine at codon 113 and aspartic acid to asparagine at codon 114). B*5708 differed from B*570101 by a single substitution (G to C) at position 247 in exon 2 causing an amino acid difference between B*570101 and B*5708 products of arginine to proline at codon 83. The likely haplotypes bearing these alleles were identified. Both alleles occurred once in approximately 25,000 random blood donors so both have a frequency of approximately 0.00002 (carriage frequency 0.004%). B*4414 and B*5708 specificities both gave 'short' serological reactivity for their expected specificities and Bw4. The likely reasons for this are discussed in relation to the epitopes of B44 and B57.     

Characterization of a new HLA-B18 allele, B*1806, which lacks expression of the Bw6 epitope

Abstract: HLA-B18 is a well defined Bw6-associated serologic specificity. Up to now, four different sequences have been characterised in Caucasian populations (B*1801,3,4,5), and one in Orientals (B*1802). We report a new HLA-B18 subtype (B*1806) which was serologically detected in a Spanish Caucasian individual as a B18 Bw4-associated antigen. Complete coding region sequencing showed that B*1806 differs from B*1801 in a unique nu-cleotide at position 299 (A to T), giving rise to an amino acid replacement in residue 76 (glutamic acid to valine) placed at the α1 domain. Therefore, in contrast to the serologic results, B*1806 possesses the canonical Bw6 motif at position 77–83. Subsequent flow cytometric assays proved that B*1806 evidences neither Bw4 nor Bw6 epitopes. Only three additional HLA-B alleles encode valine at codon 76, B*4601, B*7301 and B*5503, and like B*1806, all of them would include a Bw6 motif associated to the negative recognition by Bw6 antibodies. These findings support that valine at position 76 will modify the Bw6 epitope drastically, and suggest that this group of HLA-B alleles would define a third, Bw4 and Bw6-negative, lineage of molecules. Furthermore, valine 76 will also prevent the binding of Bw6 antibodies to those HLA-C antigens with the canonical Bw6 epitope (Cw*1,3,7,8,12,13,14,16).     

Immunogenetics of a new HLA‐B null allele,HLA‐B*4423N

The second example of an HLA‐B*44 null allele (B*4423N) was identified by discrepancies between serological and polymerase chain reaction–sequence‐specific primer (PCR‐SSP) typing in two north‐western European Caucasoid unrelated stem cell donor volunteers. HLA‐B*4423N was identical to B*440201 except for a single nucleotide substitution at position 493 in exon 3, resulting in a premature stop codon at bases 493–495 (TAG rather than CAG at codon 141). As expected, comprehensive serological testing using 54 antisera, directed towards B44 or Bw4, failed to identify the HLA‐B44 (Bw4) specificity. The B*4423N‐bearing haplotype was identified as A*0201, Cw*0501, DRB1*0408, DRB4*01, DQA1*03, DQB1*0304 and the frequency of B*4423N estimated as 0.00006 (carriage frequency 0.0121%) in 16 533 subjects resident in Wales.     

Identification of a novel HLA-B*2722 allele from a Filipino cell

We present the novel HLA-allele B*2722 amplified and sequenced from a Filipino individual. This DNA was included several times in the International Cell Exchange, UCLA, and typed at the time as B*27 or B*2706 by the majority of the participating laboratories. The second HLA-B allele of this person is B*3802. B*2704/06 or B*2704/06/10 were suggested by approximately one-third of the laboratories. As we were investigating the intron 3 sequences of B*27 alleles, we also sequenced exon 4 of this Filipino DNA and found a single nucleotide exchange in exon 4 (pos. 704) which was not in concordance with the previous B*2706 typing. Our sequencing results showed that the coding sequence of B*2722 is identical to B*2706 in exon 1, 2 and 3. In exon 4 the B*2722 sequence is identical to B*2704. HLA-B*2704 differs from B*2706 in one base at position 704, a G in B*2704 and a C in B*2706, respectively.