Identification of three novel HLA class I alleles: HLA-B*3928, HLA-B*400104 and HLA-B*4437

Three new human leukocyte antigen (HLA) class I alleles have been identified in the Tissue Typing Laboratory in Sydney, Australia. Sequence analysis of exon 2 and exon 3 of the HLA-B gene revealed the novel polymorphism. A silent substitution of C to T at nucleotide position 369 has been identified for the HLA-B*400104 allele when compared to the closest matched allele, HLA-B*400101. The HLA-B*3928 allele was identified with a nucleotide substitution of G to C at position 362 when compared to the closest matched allele, HLA-B*390101, resulting in an amino acid substitution of Arginine to Threonine. A nucleotide substitution of C to G at position 572 resulting in the amino acid change Serine to Tryptophan was identified in the new allele HLA-B*4437, when compared to the closest matched allele HLA-B*440301. Both amino acid substitutions implicate a different specificity and affinity of antigen binding for the alleles HLA-B*3928 and HLA-B*4437.     

Characterization of a novel allele HLA-B*3549

A novel HLA-B allele, B*3549, was identified in a bone marrow transplantation candidate. B*3549 differs from B*3525 by two nucleotides at exon 2, position 142 (T to G) and 165 (G to C). The difference at position 142 resulted in an amino acid difference (serine to alanine). However, the difference at position 165 did not cause any amino acid change. This novel allele was found on a haplotype with A*3101, B*3549, Cw*0401, DRB1*0407, and DQB1*0302.     

Molecular, serological and population studies on a novel HLA-B allele — HLA-B*5002

Abstract: A novel HLA-B allele (B*5002), detected as a discrepancy between serological and PCR-SSP HLA-A and B phenotyping of bone marrow panel donors, was identified by nucleotide sequencing of exons 2 and 3. Titration studies on 39 HLA-B12/B21 cross-reactive antisera showed that the serological specificity of HLA-B*5002 was HLA-B45. PCR-SSP testing of 287 serologically defined HLA-B45-positive subjects from a panel of 12,411 donors, together with HLA-B*45 and B*5002 frequency data on 4,342 PCR-SSP typed subjects, indicated that 4.53% of serologically defined HLA-B45-positive subjects possess HLA-B*5002 and not HLA-B*4501. The pheno-type frequency of HLA-B*5002 was 0.08954%; gene frequency was 0.00045 ( n =16,753). In 73.3% of instances B*5002 appeared to be present on a haplotype with DRBl*0406 and DQB1*0402, 54.6% of which possessed A*2301. The B*5002, DRBl*0406, DQB1*0402 haplotype represents 52.4% of all haplotypes with DRB1*04 and DQB1*04 and 78.6% of haplotypes possessing DRBl*0406 and DQBl*0402.     

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 new HLA-DRB1 allele, HLA-DRB1*1212, and confirmation of HLA-B*1586*

A novel allele, HLA-DRB1*1212, was identified by sequence-based typing. DRB1*1212 was identical to DRB*120101 at exon 2 except for a single nucleotide at position 199 from A to C, leading to amino acidic substitution from Ile to Leu at codon 67. We also confirmed the HLA-B*1586 in another Chinese person.     

Identification of two new alleles in a single Korean individual,HLA-B*1568 and HLA-DRB1*1208

We have identified a new HLA-B*15 allele and a new HLA-DRB1*12 allele, named B*1568 and DRB1*1208, respectively. The alleles were identified using a combination of sequence specific primers, reverse line sequence specific oligonucleotide probing and sequence-based typing. Both alleles were identified in a single individual of Korean origin. HLA-B*1568 appears to be an HLA-B*4801/B*1507 hybrid combining the exon 2 sequence of B*4801 and the exon 3 and 4 sequences of B*1507. Exon 2 of DRB1*1208 was most similar to DRB1*1201 or 1206, with a single mismatch at nucleotide position 165 (A to C). At the protein level, this substitution results in a phenylalanine substitution at position 26 that creates an identical amino acid sequence to DRB3*0202 between amino acid positions 17 and 36.     

Sequence, genetics and serology of a new HLA-B allele: B*4903

A new HLA-B allele - B*4903 - was detected by the polymerase chain reaction using sequence-specific priming (PCR-SSP), in a Caucasoid bone marrow panel donor, that differs from B*4901 by 8 nucleotides at positions 141, 142, 144, 165, 167, 193, 206 and 213 in exon 2. These substitutions all occur in HLA-B*51 and B*52 alleles and encode 4 amino acid substitutions at positions 24 (Thr to Ala), 32 (Leu to Gln), 41 (Thr to Ala) and 45 (Lys to Thr). This suggests that B*4903 occurred following a gene conversion-like event involving B*4901 and probably a B*51 allele. HLA-B*4903 was identified on a haplotype with: HLA-A*0201; Cw*07; DRB1*1302/34; DRB3*0301; DQA1*0102; DQB1*0604; BfS; C4A3; C4BQ0 and encodes a unique serological specificity which was characterised by the reactivity of 55 antisera directed towards at least four predicted epitopes. No further examples of B*4903 were found in 15,796 consecutive HLA PCR-SSP typed donors from the Welsh Bone Marrow Donor Registry, indicating that this allele has a phenotype frequency of <0.01% and a gene frequency of <0.00004.     

Characterization of HLA-B*5516, -B*1313, -B*9512, and -DRB1*1457 alleles identified in a southwest Chinese population

The human leukocyte antigen (HLA)-B*5516 allele differs from the B*5502 by a single 97 T --> C substitution (His to Tyr at position 33) in exon 2. The B*1313 allele results from 419 T --> A and 420 A --> C substitutions, encoding a Leu to Tyr substitution at 140 in exon 2 of the B*1301 allele. The B*9512 allele differs from B*1502 by a single 360 G --> C substitution (Gln to His at 120) in exon 3. The DRB1*1457 allele appears to be a hybrid molecule generated by recombination between the DRB1*13 and DRB1*14 alleles. The serological equivalents of these new alleles are HLA-B22, -B13, -B15, and DR13, respectively. Family studies detected two rare haplotypes: A*11, B*9512, DRB1*14 and A*24, B*52, Cw*07, DRB1*1457, DRB3*020201, DQB1*050301. The gene frequencies of these alleles in the Chinese population are less than 0.0001.     

HLA-A, HLA-B, and HLA-DRB1 allele distribution in a large Armenian population sample

Human leukocyte antigen (HLA)-A, HLA-B, and HLA-DRB1 gene frequencies were investigated in 4279 unrelated Armenian bone marrow donors. HLA alleles were defined by using PCR amplification with sequence specific primers (PCR-SSP) high- and low-resolution kits. The aim of this study was to examine the HLA diversity at the high-resolution level in a large Armenian population sample, and to compare HLA allele group distribution in Armenian subpopulations. The most frequently observed alleles in the HLA class I were HLA-A*0201, A*0101, A*2402, A*0301, HLA-B*5101, HLA-B*3501, and B*4901. Among DRB1 alleles, high frequencies of DRB1*1104 and DRB1*1501 were observed, followed by DRB1*1101 and DRB1*1401. The most common three-locus haplotype found in the Armenian population was A*33-B*14-DRB1*01, followed by A*03-B*35-DRB1*01. Our results show a similar distribution of alleles in Armenian subpopulations from different countries, and from different regions of the Republics of Armenia and Karabagh. The low level of genetic distances between subpopulations indicates a high level of population homogeneity, and the genetic distances between Armenians and other populations show Armenians as a distinct ethnic group relative to others, reflecting the fact that Armenians have been an 'isolated population' throughout centuries. This study is the first comprehensive investigation of HLA-allele group distribution in a subset of Armenian populations, and the first to provide HLA-allele and haplotype frequencies at a high-resolution level. It is a valuable reference for organ transplantation and for future studies of HLA-associated diseases in Armenian populations.     

Analysis of tumor necrosis factor-alpha promoter polymorphism in type 1 diabetes: HLA-B and -DRB1 alleles are primarily associated with the disease in Japanese

Polymorphisms in the 5'-flanking region of the tumor necrosis factor (TNF)-alpha gene were examined to study the genetic background of type 1 diabetes in Japanese. Five different biallelic polymorphisms were examined in 136 type 1 diabetic patients and 300 control subjects. The frequencies of individuals carrying TNF-alpha-857T allele (designated as TNFP-D allele) or -863A/-1,031C allele (designated as TNFP-B allele) were significantly increased in the patients as compared with the controls. Since these TNF-alpha alleles are in linkage disequilibria with certain DRB1 and HLA-B alleles, two-locus analyses were carried out. The TNFP-D allele did not increase the risk in either the presence or absence of the DRB1*0405 or HLA-B54 allele, while the DRB1*0405 and HLA-B54 alleles per se could confer susceptibility in both the TNFP-D allele-positive and -negative populations. Moreover, an odds ratio was remarkably elevated in the population carrying both DRB1*0405 and HLA-B54. Similarly, the TNFP-B allele did not show significant association with the disease in either the HLA-B61-positive or -negative population, while the HLA-B61 allele could significantly increase the risk in the TNFP-B allele-positive population. These data suggest that the associations of TNFP-D and -B alleles may be secondary to their linkage disequilibria with the susceptible HLA class I and class II alleles. Because HLA-B and DRB1 genes were independently associated, both of these genes may be contributed primarily to the pathogenesis of type 1 diabetes in Japanese.     

Identification of a new HLA-B*08 variant, HLA-B*0804

The HLA-B locus is the most polymorphic locus known with currently over 100 different alleles described. Many of these alleles encode variants of the serologically-defined tissue transplantation antigens. This high level of diversity makes accurate tissue typing difficult. Here we present the sequence of a new HLA-B *08 variant, HLA-B *0804. found in Caucasian siblings JH and PF serologically typed as HLA-B51/B59 and HLA-B59/B60, respectively. Additionally, DNA-based typing by the polymerase chain reaction using sequence-specific primers (PCR-SSP) identified HLA-B *51 in JH and HLA-B *4001 in PF. However, PCR-SSP failed to identify a second allele in either of these individuals. The unusual finding of a B59 antigen in a Caucasian and the discrepant molecular typing results suggested that these individuals might express novel HLA molecules. Using denaturing gradient gel electrophoresis (DGGE) followed by direct sequencing, we characterized a novel HLA-B *08 variant, HLA-B *0804. The presence of this allele was confirmed by cloning and sequencing. HLA-B *0804 differed from HLA-B *0801 by only one nucleotide substitution resulting in an amino acid replacement of phenylalanine by serine at position 67. Incidentally, this single nucleotide difference was sufficient to prevent amplification by PCR-SSP. This striking difference between both the serologically typed antigen and the PCR-SSP-identified allele compared to the sequenced allele supports the use of sequence-based typing for the analysis of HLA class I locus alleles.     

Identification of a novel HLA-B allele, HLA-B*3713, in a Chinese individual

A novel human leukocyte antigen (HLA) class I allele, HLA-B*3713, has been identified in a Chinese individual. The HLA-B*3713 allele differs from the closest matching allele B*370101 by one nucleotide substitutions in exon 3 at nt 527(T-->A), resulting in an amino acid change from Val (GTG) to Glu (GAG) at codon 152.     

Identification of a novel allele HLA-B*5610 in a Chinese potential bone marrow donor

A novel HLA-B allele, B*5610, has been identified in a potential bone marrow donor, his mother and brother using DNA-based typing and molecular cloning methods. The B*5610 allele differs from the closest matching HLA sequence of B*5602 by two nucleotide substitutions in exon 3, 559 C-->A and 560 T-->C, resulting in an amino acid change from Leu (CTG) to Thr (ACG) at codon 187. This new allele was segregated together with A*24020101 and DRB1*140101 in the proband's family. Serology study revealed that B*5610 is associated with B22 specificity. A PCR-SSP method was developed to distinguish B*5610 from other B*56 alleles. No further individuals with B*5610 were detected in 5000 Chinese bone marrow blood donors.     

Analysis of HLA-B*44 alleles encoded on extended HLA haplotypes by direct automated sequencing

Abstract: We developed a PCR-based approach to sequence exons 2 and 3 of HLA-B44 alleles from genomic DNA. We applied this method to determine the B44 alleles encoded on extended HLA-A, B, DRB1, DQB1 haplotypes and the degree of mismatching for B44 alleles among marrow transplant patients and their unrelated donors (URD). A total of 81 samples was studied and included 38 patients, 42 donors and the cell "FMB"; the 80 clinical samples were comprised of 8 unpaired patients, 12 unpaired donors, and 30 URD-recipient pairs. Three alleles encoding B44 were identified, B*4402 (N=51), 4403 (N=32) and a new allele designated B*44KB and named B*4405 (N=4). Of the 27 patients for whom family study was available, there were 13 different B*4402, 7 different B* 4403 and 2 new B*4405 haplotypes. HLA-A2, Cw*0501, B*4402, DRB1* 0401, DQB1*0301 (n=2); A2, Cw*0501, B*4402, DRB1*1501, DRB5* 0101, DQB1*0602 (n=2); and HLA-A29, Cw*1601, B*4403, DRB1* 0701, DQB1*0201 (n=5) comprised the most common patient haplotypes. Of 30 URD-recipient transplant pairs studied, 27 were HLA-A, B serologically matched and DRB1, DRB3, DRB5, DQB1 allele matched, and 3 pairs were DRB1-mismatched. All B44 allele mismatching (N=3) occurred among the 27 matched pairs. The novel B*4402-variant sequence, HLA-B*4405, was identified in 4 individuals, and in each case was associated with an HLA-B44, Cw*02022, DRB1*0101, DQB1*0501 haplotype. HLA-B*4405 and B*4402 are identical in exon 2; in exon 3 however, B*4405 encodes T instead of G at nucleotide position 75 which translates to a substitution of tyrosine for aspartic acid at codon 116. Finally, the published B*4402 sequence derived from cell "FMB" was found to contain an error; the corrected B*4402 sequence encodes G rather than C at position 146 of exon 3.     

A novel HLA-B*55 allele, HLA-B*5514, found in a DNA sample derived from a bone marrow donor

In this study, we report the identification of a new human leucocyte antigen-B (HLA-B) allele in a sample that was found in our routine typing. This novel allele, officially designed HLA-B*5514, was found in a male donor of Bavarian Caucasoid origin (Laboratory code: 117562) typed in order for a request of the bone marrow donor registry Aktion Knochenmarkspende Bayern. Although this novel allele was added to the HLA-B*55 family by the Nomenclature Committee, the next related alleles were found in the HLA-B*56 group; HLA-B*5612 differing in six positions from HLA-B*5514 is the closest related allele.     

Identification of a novel HLA-B allele, HLA-B*5529, by haplotype-specific sequencing

We have identified a novel HLA-B allele, B*5529. The novel allele differs from HLA-B*5501 by a single nucleotide substitution at codon 479 in exon 3 resulting in an amino acid change from alanine to valine. This alteration neither affects the peptide binding site nor the T-cell receptor (TCR) contact residues. Thus, the newly found allele is estimated to have a low alloreactive potential in case of a mismatch to the most common HLA-B allele B*5501.     

序列分析及确认HLA新等位基因B*55:46

背景：近几年来,随着中华骨髓库的建立和人类白细胞抗原分型技术的不断发展和提高,中国人类白细胞抗原新等位基因不断被发现。 目的：探索中国人的人类白细胞抗原新等位基因。 方法：应用PCR-序列特异性寡核苷酸探针基因分型技术,对1名27岁男性汉族造血干细胞志愿捐献者进行HLA基因分型,并应用基于测序的方法分析该基因序列及与最相近等位基因序列的差异。 结果与结论：PCR-序列特异性寡核苷酸探针结果显示该样本HLA-B基因座反应格局出现异常提示;基因测序结果表明其B基因座第3外显子序列与所有已知HLA-B等位基因序列均不一致,在所检测的第2、3外显子中,与序列最相近的等位基因B*55:02:01的差异只是在第3外显子发生了nt 412 A→G一个核苷酸替代,导致第138位密码子由AAC→GAC,相应的编码的天冬酰胺改变为天冬氨酸。将其序列提交国际基因数据库及IMGT/HLA 数据库,证实该HLA等位基因为国际上首次发现,被世界卫生组织织人类白细胞抗原因子命名委员会正式命名为HLA-B*55:46 (HM989018)。     

Identification of two novel alleles HLA-B*3569 and -B*4450 and confirmation of HLA-A*2631 in the Brazilian population

Two novel alleles, human leukocyte antigen (HLA)-B*3569, -B*4450 and a confirmatory sequence of HLA-A*2631 were identified during a routine typing for the Brazilian Bone Marrow Donor Registry. Sequence analysis of coding exons 2 and 3 revealed a single nucleotide substitution in HLA-B*3569 and two single nucleotide substitutions in HLA-B*4450, compared with closely related alleles. At the protein level, these substitutions result in a change of a single amino acid residue in each of HLA-B*3569 and -B*4450 at positions 74 (Arg > Pro) and 80 (Thr > Ile), respectively. These variations are located in the highly polymorphic region at the end of the alpha(1) domain of the HLA molecule. It appears that HLA-B*3569 arose from the analogous HLA-B*3510 through a point mutation. However, HLA-B*4450 may have arisen from HLA-B*440301 and -B*4425 by gene conversion.     

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.     

A single amino acid exchange shifts the serological reactivity of the novel HLA-B*4442 allele product from HLA-B44 to HLA-B21

A novel HLA-B (human leukocyte antigen-B) allele, HLA-B*4442, was identified both in a Czech patient with leukaemia and in his mother. The presence of a novel allele was initially suspected because conflicting results were obtained by serological and DNA typing techniques. The HLA typing using the polymerase chain reaction-sequence-specific primers (PCR-SSP) at the two-digit level indicated an allele belonging to the HLA-B*44 group, whereas serological typing indicated HLA-B21. Typing with PCR-sequence-specific oligonucleotides (PCR-SSO) resulted in a unique reaction pattern that could not be assigned to a known allele, PCR-SSP typing at the four-digit level did not match any known B*44 allele, either. The sequencing-based typing of the HLA-B locus then revealed the novel B*4442 allele that is identical with B*4405 except a single C-->G nucleotide exchange at position 572. This exchange results in an amino acid substitution from serine to tryptophan at position 167 of the expressed HLA-B protein. The B21 serological reactivity of the novel B*4442 allele product was confirmed by employing an additional serological panel of typing sera. Our findings support previous reports claiming that serine at the position 167 in the alpha-2 domain of the HLA-B protein is a major determinant of the HLA-B44(12) serological epitope.