Nomenclature for factors of the HLA system, 2000

25 years of the IPD-IMGT/HLA Database

Twenty-five years ago, in 1998, the HLA Informatics Group of the Anthony Nolan Research Institute released the IMGT/HLA Database. Since this time, this online resource has acted as the repository for the numerous variant sequences of HLA alleles named by the WHO Nomenclature Committee for Factors of the HLA System. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this work. During this time, the technology underlying HLA typing has undergone significant changes. Next generation sequencing (NGS) has superseded previous methodologies of HLA typing and can generate large amounts of high-resolution sequencing data. This has resulted in a drastic increase in the number and complexity of sequences submitted to the database. The challenge for the IPD-IMGT/HLA Database has been to maintain the highest standards of curation, while supporting the core set of tools and functionality to our users with increased numbers of submissions and sequences. Traditional methods of accessing and presenting data have been challenged and new methods utilising new computing technologies have had to be developed to keep pace and support a shifting user demographic.

Predominant frequency of HLA-B*27 in patients with ankylosing spondylitis in southeastern China

OBJECTIVES

This study was to investigate the polymorphism and distribution of alleles of HLA-B*27 in patients with ankylosing spondylitis (AS) in Han population of southeastern China.

METHODS

A total of 89 peripheral blood samples from southeastern Chinese Han patients with AS that diagnosed according to Modified New York criteria were subtyped using the high-resolution PCR-SSP.Exon 2-3 of HLA-B*27 gene was amplified and sequenced to further confirm the HLA-B*27 subtype.

RESULTS

The frequency of HLA-B*27 was 99.87% in AS patients. Three subtypes, HLA-B*2704, HLA-B*2705, and HLA-B*2706 were identified. The frequencies for these three alleles were HLA-B*2704 in 84/88 (95.46%), HLA-B*2705 in 3/88(3.41%), and HLA-B*2706 in 1/88 (1.13%) of the HLA-B*27 positive patients, respectively.

CONCLUSIONS

Our study shows that HLA-B*2704 has an overwhelming frequency in southeastern Chinese Han AS patients. A combined analysis including previous studies of HLA-B*27-subtype distributions in Chinese Han populations showed that HLA-B*2704 may originate from the southern Han and then migrate and spread to the northern areas, and HLA-B*2705 show the opposite result.

SARS-CoV-2 Vaccines Based on the Spike Glycoprotein and Implications of New Viral Variants

Coronavirus 19 Disease (COVID-19) originating in the province of Wuhan, China in 2019, is caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), whose infection in humans causes mild or severe clinical manifestations that mainly affect the respiratory system. So far, the COVID-19 has caused more than 2 million deaths worldwide. SARS-CoV-2 contains the Spike (S) glycoprotein on its surface, which is the main target for current vaccine development because antibodies directed against this protein can neutralize the infection. Companies and academic institutions have developed vaccines based on the S glycoprotein, as well as its antigenic domains and epitopes, which have been proven effective in generating neutralizing antibodies. However, the emergence of new SARS-CoV-2 variants could affect the effectiveness of vaccines. Here, we review the different types of vaccines designed and developed against SARS-CoV-2, placing emphasis on whether they are based on the complete S glycoprotein, its antigenic domains such as the receptor-binding domain (RBD) or short epitopes within the S glycoprotein. We also review and discuss the possible effectiveness of these vaccines against emerging SARS-CoV-2 variants.

IPD-IMGT/HLA Database

The IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, currently contains over 25 000 allele sequence for 45 genes, which are located within the Major Histocompatibility Complex (MHC) of the human genome. This region is the most polymorphic region of the human genome, and the levels of polymorphism seen exceed most other genes. Some of the genes have several thousand variants and are now termed hyperpolymorphic, rather than just simply polymorphic. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this information, providing the scientific and medical community access to the many variant sequences of this gene system, that are critical for the successful outcome of transplantation. The number of currently known variants, and dramatic increase in the number of new variants being identified has necessitated a dedicated resource with custom tools for curation and publication. The challenge for the database is to continue to provide a highly curated database of sequence variants, while supporting the increased number of submissions and complexity of sequences. In order to do this, traditional methods of accessing and presenting data will be challenged, and new methods will need to be utilized to keep pace with new discoveries.

The role of demographic history and selection in shaping genetic diversity of the Galápagos penguin (Spheniscus mendiculus)

Although many studies have documented the effects of demographic bottlenecks on the genetic diversity of natural populations, there is conflicting evidence of the roles that genetic drift and selection may play in driving changes in genetic variation at adaptive loci. We analyzed genetic variation at microsatellite and mitochondrial loci in conjunction with an adaptive MHC class II locus in the Galápagos penguin (Spheniscus mendiculus), a species that has undergone serial demographic bottlenecks associated with El Niño events through its evolutionary history. We compared levels of variation in the Galápagos penguin to those of its congener, the Magellanic penguin (Spheniscus magellanicus), which has consistently maintained a large population size and thus was used as a non-bottlenecked control. The comparison of neutral and adaptive markers in these two demographically distinct species allowed assessment of the potential role of balancing selection in maintaining levels of MHC variation during bottleneck events. Our analysis suggests that the lack of genetic diversity at both neutral and adaptive loci in the Galápagos penguin likely resulted from its restricted range, relatively low abundance, and history of demographic bottlenecks. The Galápagos penguin revealed two MHC alleles, one mitochondrial haplotype, and six alleles across five microsatellite loci, which represents only a small fraction of the diversity detected in Magellanic penguins. Despite the decreased genetic diversity in the Galápagos penguin, results revealed signals of balancing selection at the MHC, which suggest that selection can mitigate some of the effects of genetic drift during bottleneck events. Although Galápagos penguin populations have persisted for a long time, increased frequency of El Niño events due to global climate change, as well as the low diversity exhibited at immunological loci, may put this species at further risk of extinction.

HLA-HD: An accurate HLA typing algorithm for next-generation sequencing data

The accurate typing of human leukocyte antigen (HLA) alleles is critical for a variety of medical applications, such as genomic studies of multifactorial diseases, including immune system and inflammation-related disorders, and donor selection in organ transplantation and regenerative medicine. Here, we developed a new algorithm for determining HLA alleles using next-generation sequencing (NGS) results. The method consists of constructing an extensive dictionary of HLA alleles, precise mapping of the NGS reads, and calculating a score based on weighted read counts to select the most suitable pair of alleles. The developed algorithm compares the score of all allele pairs, taking into account variation not only in the domain for antigen presentation (G-DOMAIN), but also outside this domain. Using this method, HLA alleles could be determined with 6-digit precision. We showed that our method was more accurate than other NGS-based methods and revealed limitations of the conventional HLA typing technologies. Furthermore, we determined the complete genomic sequence of an HLA-A-like-pseudogene when we assembled NGS reads that had caused arguable typing, and found its identity with HLA-Y*02:01. The accuracy of the HLA-A allele typing was improved after the HLA-Y*02:01 sequence was included in the HLA allele dictionary.

Association of polymorphisms of the transporter associated with antigen processing (TAP2) gene with pulmonary tuberculosis in an elderly Japanese population

The transporter associated with antigen processing 2 (TAP2) gene is involved in the immunological response to tuberculosis (TB) infection. Variations in the TAP2 gene have been associated with TB infection in small population studies in India, Columbia, and Korea. We investigated the association of TAP2 polymorphisms with TB susceptibility in an elderly Japanese population. We analyzed samples from consecutive autopsy cases (n = 1850) registered in the Japanese Geriatric SNP Research database. TB was diagnosed pathologically by TB granuloma on autopsy samples. There were 289 cases and 1529 controls. Twenty-four single nucleotide variations (SNVs), including four missense variations in the TAP2 region, were genotyped using the Illumina Infinium Human Exome BeadChip array. Of the 24 SNVs in the TAP2 gene, rs4148871, rs4148876 (R651C), and rs2857103 showed statistically significant associations with TB susceptibility, and rs4148871 and rs2857103 also showed significant genotypic associations in a dominant allele model adjusted for age, sex, and smoking. Haplotype analysis showed that TAP2 allele *0103 conferred an increased TB risk (OR = 1.48, p = 0.0008), while the TAP2 *0201 allele was protective against TB (OR = 0.73, p = 0.0007). Our results suggest that TAP2 polymorphisms influence TB susceptibility in a Japanese population.

IMGT/HLA and the Immuno Polymorphism Database

The IMGT/HLA Database (http://www.ebi.ac.uk/ipd/imgt/hla/) was first released over 15 years ago, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic, with some genes currently having over 3,000 known allelic variants. The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) expands on this model, with a further set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. IPD currently consists of four databases: IPD-KIR contains the allelic sequences of killer-cell immunoglobulin-like receptors; IPD-MHC is a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/.

The IMGT/HLA database

It is 14 years since the IMGT/HLA database was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Of these, 21 genes encode proteins of the immune system that are highly polymorphic. The naming of these HLA genes and alleles and their quality control is the responsibility of the World Health Organization Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to these data through the website http://www.ebi.ac.uk/imgt/hla/. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the HLA community and the wider research and clinical communities. This article describes the latest updates and additional tools added to the IMGT/HLA project.

MHC diversity and mate choice in the magellanic penguin, Spheniscus magellanicus

We estimated levels of diversity at the major histocompatibility complex (MHC) class II DRß1 gene in 50 breeding pairs of the Magellanic penguin and compared those to estimates from Humboldt and Galapagos penguins. We tested for positive selection and 2 conditions required for the evolution of MHC-based disassortative mating: 1) greater MHC diversity between breeding pairs compared to random mating, and 2) associations between MHC genotype and fitness. Cloning and sequencing of the DRß1 gene showed that Magellanic penguins had higher levels of genetic variation than Galapagos and Humboldt penguins. Sequence analysis revealed 45 alleles with 3.6% average proportion of nucleotide differences, nucleotide diversity of 0.030, and observed heterozygosity of 0.770. A gene phylogeny showed 9 allelic lineages with interspersed DRß1 sequences from Humboldt and Galapagos penguins, indicating ancestral polymorphisms. d (N)/d (S) ratios revealed evidence for positive selection. Analysis of breeding pairs showed no disassortative mating preferences. Significant MHC genotype/fitness associations in females suggest, however, that selection for pathogen resistance plays a more important role than mate choice in maintaining diversity at the MHC in the Magellanic penguin. The differential effect of MHC heterozygosity on fitness between the sexes is likely associated with the relative role of hatching and fledging rates as reliable indicators of overall fitness in males and females.

Nonequivalence of classical MHC class I loci in ability to direct effective antiviral immunity

Structural diversity in the peptide binding sites of the redundant classical MHC antigen presenting molecules is strongly selected in humans and mice. Although the encoded antigen presenting molecules overlap in antigen presenting function, differences in polymorphism at the MHC I A, B and C loci in humans and higher primates indicate these loci are not functionally equivalent. The structural basis of these differences is not known. We hypothesize that classical class I loci differ in their ability to direct effective immunity against intracellular pathogens. Using a picornavirus infection model and chimeric H-2 transgenes, we examined locus specific functional determinants distinguishing the ability of class I sister genes to direct effective anti viral immunity. Whereas, parental FVB and transgenic FVB mice expressing the H-2K^b gene are highly susceptible to persisting Theiler's virus infection within the CNS and subsequent demyelination, mice expressing the D^b transgene clear the virus and are protected from demyelination. Remarkably, animals expressing a chimeric transgene, comprised primarily of K^b but encoding the peptide binding domain of D^b, develop a robust anti viral CTL response yet fail to clear virus and develop significant demyelination. Differences in expression of the chimeric K^bα1α2D^b gene (low) and D^b (high) in the CNS of infected mice mirror expression levels of their endogenous H-2^q counterparts in FVB mice. These findings demonstrate that locus specific elements other than those specifying peptide binding and T cell receptor interaction can determine ability to clear virus infection. This finding provides a basis for understanding locus-specific differences in MHC polymorphism, characterized best in human populations.

MHC I genes are best understood as regulators of antiviral immunity. In humans and mice there are 2 to 3 homologous MHC I genes encoding highly polymorphic antigen presenting molecules which present virus proteins to T lymphocytes. A world wide effort has catalogued more than 6,300 classical HLA MHC I alleles in human populations, making these MHC loci among the best characterized polymorphic gene families. However, there has been little progress in understanding implications of the differences in polymorphism present at the HLA A, B, and C loci. By expressing MHC I molecules capable of presenting viral antigens under regulatory determinants from different sister MHC I genes of the mouse, we address the hypothesis that locus-specific differences in the regulation of the homologous MHC I sister genes can determine whether alleles at any particular locus can effectively target protective immunity against virus infection. We find that while the ability to activate cellular immune effectors is determined by the highly polymorphic MHC I sequences encoding the peptide binding domain, the ability of these T lymphocytes to effectively clear virus from the central nervous system can also be determined by gene sequences mapping outside of this region.

Standard methods for the management of immunogenetic data

In this chapter, we outline some basic principles for the consistent management of immunogenetic data. These include the preparation of a single master data file that can serve as the basis for all subsequent analyses, a focus on the quality and homogeneity of the data to be analyzed, the documentation of the coding systems used to represent the data, and the application of nomenclature standards specific for each immunogenetic system being evaluated. The data management principles discussed here are intended to provide a foundation for the data analysis methods detailed in Chaps. 13 and 14 . The relationship between the data management and analysis methods covered in these three chapters is illustrated in Fig. 3.The application of these data management principles is a first step toward consistent and reproducible data analyses. While it may take extra time and effort to apply them, we feel that it is better to take this approach than to assume that low data quality can be compensated for by large sample sizes.In addition to their relevance for analytical reproducibility, it is important to consider these data management principles from an ethical perspective. The reliability of the data collected and generated as part of a research study should be as important a component of the ethical review of a research application as the security of those data. Finally, in addition to ensuring the integrity of the data from collection to publication, the application of these data management principles will provide a means to foster research integrity and to improve the potential for collaborative data sharing.

A frame shift due to a two-nucleotide deletion results in an HLA-B null allele, B*9549N

This report describes the identification of a new human leukocyte antigen (HLA) class I null allele, B*9549N, resulting from a premature stop codon in exon 3.

Analysis of the complete genomic sequence of HLA-A alleles in the Chinese Han population

To analyse the complete genomic sequences and investigate the intron polymorphism of the human leucocyte antigen (HLA)-A locus, the full-length nucleotide sequences of each major allelic group of HLA-A in the Chinese Han population were determined, including HLA-A*01, A*02, A*03, A*11, A*23, A*24, A*26, A*29, A*30, A*31, A*32, A*33, A*34, A*68, A*69. More than 3.0-kb DNA fragment of HLA-A locus was amplified from 5'-untranslated region to 3'-noncoding region for sequencing. Full-length sequences of the HLA-A alleles were determined using an ABI BigDye((R)) Terminator Cycle Sequencing kit and the HLA-A phylogenetic tree was analysed by dnaman software. Full-length nucleotide sequences of 15 HLA-A alleles (GenBank Accession numbers EU445470-EU445484) were obtained. HLA-A*110101, A*2301, A*300101, A*310102, A*330301, A*340101, A*680102 and A*6901 alleles were firstly reported for complete genomic sequences. Total 247 polymorphism positions were found in the complete genomic sequences of HLA-A alleles and a insertion of 17 nucleotides within intron 3 was observed in several allelic groups. According to the phylogenetic tree of the full-length nucleotide sequences, HLA-A locus was classified into seven major allelic lineages. In this study, complete genomic sequences of common HLA-A alleles were obtained and the data will help us understand the evolution of HLA-A.

Identification of a novel HLA-DRB allele, HLA-DRB1*1461

We describe the identification of a new DRB1*14 allele, DRB1*1461, found in a Chinese individual. The novel allele has been identified in routine polymerase chain reaction-sequence-specific oligonucleotide and sequence-based typing. The nucleotide sequence of DRB1*1461 is identical to DRB1*1404 except for a single substitution in codon 16 (TAT-->CAT), leading to a change from Tyr to His.

Outcome of non-T-cell-depleted HLA-haploidentical hematopoietic stem cell transplantation from family donors in children and adolescents

Non-T-cell-depleted HLA-haploidentical hematopoietic stem cell transplantation (SCT) from family members has been reported, but its effectiveness and safety are not fully known. In this study, we examined the outcomes of 83 children and adolescents with nonmalignant (n = 11) or malignant (n = 72) disorders who underwent SCT mismatched at 2 or 3 HLA loci, either from the mother (n = 56), a noninherited maternal antigen (NIMA)-mismatched sibling (n = 14), or the father/a noninherited paternal antigen (NIPA)-mismatched sibling (n = 13). Engraftment was satisfactory. Severe (grade III-IV) acute graft-versushost disease (GVHD) was noted only in malignant disease, with an incidence of 21 of 64 evaluable patients. GVHD prophylaxis with a combination of tacrolimus and methotrexate was significantly associated with a lower risk of severe acute GVHD, compared with other types of prophylaxis (P = .04). Nine of 11 patients with nonmalignant disease and 29 of 72 patients with malignant disease were alive at a median follow-up of 26 months (range, 4-57 months). Outcomes were not significantly different among the 3 donor groups (mother versus NIMA-mismatched sibling versus father/NIPA-mismatched sibling) for the malignancy disorders. Our results indicate that non-T-cell-depleted HLA-haploidentical SCT may be feasible, with appropriate GVHD prophylaxis, for young recipients who lack immediate access to a conventional stem cell source.

The IMGT/HLA database

The human leukocyte antigen (HLA) complex is located within the 6p21.3 region on the short arm of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and include many highly polymorphic HLA genes. The naming of new HLA genes and allele sequences and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. The IMGT/HLA Database acts as the repository for these sequences and is recognized as the primary source of up-to-date and accurate HLA sequences. The IMGT/HLA website provides a number of tools for accessing the database: these include allele reports, sequence alignments, and sequence similarity searches. The website is updated every 3 months with all the new and confirmatory sequences submitted to the WHO Nomenclature Committee. Submission of HLA sequences to the committee is possible through the tools provided by the IMGT/HLA Database.

Allogeneic marrow stem-cell transplantation from human leukocyte antigen-identical siblings versus human leukocyte antigen-allelic-matched unrelated donors (10/10) in patients with standard-risk hematologic malignancy: a prospective study from the French Society of Bone Marrow Transplantation and Cell Therapy

PURPOSE

To investigate the influence of donor type (human leukocyte antigen [HLA] -identical sibling donor versus HLA-A-, HLA-B-, HLA-Cw-, HLA-DRB1-, and HLA-DQB1-identical unrelated donors, or so-called 10/10) on the outcome of patients who underwent allogeneic stem-cell transplantation (alloSCT), adjusting for other prognostic factors, in patients with standard-risk hematologic malignancy.

PATIENTS AND METHODS

Between March 2000 and January 2003, we prospectively investigated the outcome of 236 consecutive patients with standard-risk malignancy from 12 French centers. Fifty-five patients underwent alloSCT from an unrelated HLA-identical donor at the allelic level, whereas 181 patients received an alloSCT from an HLA-identical sibling. Diagnoses included acute leukemia (n = 175), chronic myeloid leukemia (n = 43), and myelodysplastic syndrome (MDS; n = 18). All patients received unmodified marrow graft following myeloablative conditioning with cyclophosphamide and total-body irradiation. Graft-versus-host disease (GVHD) prophylaxis consisted of cyclosporine and short-course methotrexate in all patients.

RESULTS

In multivariable analysis, overall survival and transplantation-related mortality were adversely influenced by recipient cytomegalovirus (CMV) -positive serology, age of donor older than 37 years, and the occurrence of acute grade > or = II GVHD. Event-free survival rates were lower for patients with recipient CMV-positive serology. Acute grades II to IV GVHD rates were higher for patients with chronic myeloid leukemia (CML). No factor was found to influence either relapse or acute grades III to IV GVHD. The effect of donor type was nonsignificant for all criteria.

CONCLUSION

In patients with standard-risk malignancy, transplantation from unrelated HLA-allellically matched donors led to outcomes similar to those from HLA-identical sibling donors.

Lack of associations between HLA class II alleles and resistance to HIV-1 infection among white, non-Hispanic homosexual men

HLA class II alleles were molecularly typed for 100 high-risk seronegative men and 184 low-risk seroconverters from the Multicenter AIDS Cohort Study (MACS). Seven resistant individuals homozygous for CCR5 Delta32 deletions were excluded from analysis. In the univariate analysis, no significant HLA class II associations with resistance/susceptibility to HIV type 1 infection were identified. However, the transporter associated with antigen presentation 2 (TAP2) Ala 665 variant associated with resistance in earlier analyses in the MACS was in linkage disequilibrium with some HLA class II alleles. After adjusting for the established associations with HLA-A*0205 subgroup and TAP2 Ala 665 variant, no HLA class II alleles were independently associated with resistance/susceptibility to HIV-1 infection. Other genetic factors in the HLA class II-TAP region of the major histocompatibility complex might be involved.

Identification of a new HLA-C allele, Cw*0316, by sequence-based typing

The presence of a new allele, Cw*0316, was detected in a Caucasian individual through an unusual association. Molecular typing of the individual by sequence-specific primers and sequence-specific oligonucleotides showed the presence of B*58, B*41 and Cw*17. Sequence-based typing revealed the additional presence of another human leucocyte antigen-C allele. The new allele showed four nucleotide differences with Cw*030202 at positions 559, 560, 589 and 594 in exon 3, leading to three codon changes, codons 187, 197 and 198. This resulted in two amino acid substitutions at positions 163 (L-T) and 173 (K-E) of the mature protein, which proved sufficient to abrogate serological reactivity with Cw3-specific sera.

Identification of a novel HLA-A*0278 allele in a Chinese family

A novel human leukocyte antigen-A (HLA-A) allele, A*0278, has been identified in a Chinese family using DNA-based typing and molecular cloning methods. The alleles A*0278 differs from its closest matching HLA sequence of A*0256 by a silent substitution at 102 A > C and by two replacement substitutions, 98T > A and 292 C > G in exon 2, resulting in a change of codon 33 from Phe (TTC) to Tyr (TAC) and codon 98 from His (CAC) to Asp (GAC). Serology study revealed that A*0278 is associated with HLA-A2 broad specificity. A polymerase chain reaction-sequence-specific primers-based assay was developed to identify A*0278. Family study indicated that the propositus inhered his father's HLA haplotype A*0278, B*35, DRB1*15. No further individuals of A*0278 were found in 5000 Chinese bone marrow donor volunteers.

Identification of a novel HLA-DOB-allele, DOB*010103, by sequence-based typing in the Korean population

A new DOB allele, DOB*010103, was identified in the Korean population during sequence-based HLA-DOB typing. DOB*010103 differed from DOB*01010101 only at codon 6 (GAT-->GAC), corresponding to synonymous amino acid change (Asp-->Asp).

The HLA Dictionary 2004: a summary of HLA-A, -B, -C, -DRB1/3/4/5 and -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR and -DQ antigens

This report presents serologic equivalents of human leucocyte antigen (HLA)-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5 and -DQB1 alleles. The dictionary is an update of the one published in 2001. The data summarize equivalents obtained by the World Health Organization Nomenclature Committee for factors of the HLA System, the International Cell Exchange, the National Marrow Donor Program, recent publications and individual laboratories. This latest update of the dictionary is enhanced by the inclusion of results from studies performed during the 13th International Histocompatibility Workshop and from neural network analyses. A summary of the data as recommended serologic equivalents is presented as expert assigned types. The tables include remarks for alleles, which are or may be expressed as antigens with serologic reaction patterns that differ from the well-established HLA specificities. The equivalents provided will be useful in guiding searches for unrelated hematopoietic stem cell donors in which patients and/or potential donors are typed by either serology or DNA-based methods. The serological DNA equivalent dictionary will also aid in typing and matching procedures for organ transplant programs whose waiting lists of potential donors and recipients comprise of mixtures of serologic and DNA-based typings. The tables with HLA equivalents and a questionnaire for submission of serologic reaction patterns for poorly identified allelic products will be made available through the WMDA web page: www.worldmarrow.org. and in the near future also in a searchable form on the IMGT/HLA database.

Genetic susceptibility to type 1 diabetes in the intracellular pathway of antigen processing - a subject review and cross-study comparison

Ligand binding grooves of MHC class I molecules are able to load a panel of endogenous peptides of varying length and sequence derived from self or foreign origin to activate or deactivate cytotoxic CD8(+) T cells. Peptides are assembled with class I molecules by pathways that are either dependent or independent of transport by ABC proteins (TAP) and degradation in the immunoproteasome by its subunits LMP2 and LMP7. Those peptides that require TAP and LMP treatment appear to be subject to control and optimization by TAP for proper customizing and efficient presentation. Therefore, allelic variations in the coding sequences of TAP and LMP were suspected for a long time to be responsible for improper antigen processing, interruption of self-peptide presentation and reduced cell surface expression of MHC class I molecules resulting in the activation of autoreactive CD8(+) T cells. In this article we reviewed the controversial findings regarding the role of TAP and LMP genes in autoimmune diabetes and reevaluated data of eleven separate studies in a cross-study analysis by genotype and HLA haplotype matching. We could confirm previous results by showing that TAP2*651-A/F and TAP2*687-A/A are significantly associated with disease, independently of linkage disequilibrium (LD). LMP2-R/H surprisingly seems to be primarily disease-conferring although a weak association with DR4 serotypes can be observed. Our analysis also suggests that LMP7-B/B, TAP1-A/A and TAP2*687-A/B are the protective genotypes and that these associations are not secondary to LD with DRB1. Consequently, intracellular antigen processing associated with TAP- and proteasome-dependent pathways seems to be a critical element in T cell selection for the retention of a balanced immunity.

Allelic and haplotypic diversity of HLA-A, -B, -C, -DRB1, and -DQB1 genes in the Korean population

High-resolution human leukocyte antigen (HLA) typing exposes the unique patterns of HLA allele and haplotype frequencies in each population. In this study, HLA-A, -B, -C, -DRB1, and -DQB1 genotypes were analyzed in 485 apparently unrelated healthy Korean individuals. A total of 20 HLA-A, 43 HLA-B, 21 HLA-C, 31 HLA-DRB1, and 14 HLA-DQB1 alleles were identified. Eleven alleles (A*0201, A*1101, A*2402, A*3303, B*1501, Cw*0102, Cw*0302, Cw*0303, DQB1*0301, DQB1*0302, and DQB1*0303) were found in more than 10% of the population. In each serologic group, a maximum of three alleles were found with several exceptions (A2, B62, DR4, DR14, and DQ6). In each serologic group exhibiting multiple alleles, two major alleles were present at 62-96% (i.e. A*0201 and A*0206 comprise 85% of A2-positive alleles). Multiple-locus haplotypes estimated by the maximum likelihood method revealed 51 A-C, 43 C-B, 52 B-DRB1, 34 DRB1-DQB1, 48 A-C-B, 42 C-B-DRB1, 46 B-DRB1-DQB1, and 30 A-C-B-DRB1-DQB1 haplotypes with frequencies of more than 0.5%. In spite of their high polymorphism in B and DRB1, identification of relatively small numbers of two-locus (B-C and DRB1-DQB1) haplotypes suggested strong associations of those two loci, respectively. Five-locus haplotypes defined by high-resolution DNA typing correlated well with previously identified serology-based haplotypes in the population. The five most frequent haplotypes were: A*3303-Cw*1403-B*4403-DRB1*1302-DQB1*0604 (4.2%), A*3303-Cw*0701/6-B*4403-DRB1*0701-DQB1*0201/2 (3.0%), A*3303-Cw*0302-B*5801-DRB1*1302-DQB1*0609 (3.0%), A*2402-Cw*0702-B*0702-DRB1*0101-DQB1*0501 (2.9%), and A*3001-Cw*0602-B*1302-DRB1*0701-DQB1*0201/2 (2.7%). Several sets of allele level haplotypes that could not be discriminated by routine HLA-A, -B, and -DRB1 low-resolution typing originated from allelic diversity of A2, B61, DR4, and DR8 serologic groups. Information obtained in this study will be useful for medical and forensic applications as well as in anthropology.

Identification of a novel HLA-DQB1 allele, DQB1*0314, by sequence-based typing in the Korean population

The polymorphism of HLA class II genes is largely confined to the exon 2 region. Sequence analysis of exon 2 of the DQB1 gene revealed the novel polymorphism in the Korean population. The new DQB1 allele, DQB1*0314, was differed from DQB1*0304 only at codon 46 (GAG-->GGG), corresponding to non-synonymous amino acid change (Glu-->Gly).

Five-locus HLA typing of hematopoietic stem cell donor volunteers using PCR sequence specific primers

We have developed a strategy for five-locus human leukocyte antigen (HLA) typing of hematopoeitic stem cell (HSC) donors using the polymerase chain reaction with sequence-specific primers (PCR-SSP). The PCR-SSP method is robust, reproducible, and accurate. New PCR-SSP mixtures can be added as required and all reactions are carried out under the same conditions, which can easily be applied to the typing of other loci, e.g., ABO blood groups. Initially, 127 PCR-SSP reactions were used to detect simultaneously HLA-A, -B, -C, -DRB1/3/4/5, and DQB1 alleles, differentiated generally to the level of the first two digits of the allele name, essentially equivalent to the serological split specificity. Approximately 40% of subjects were tested against a further 29 HLA-A, -B SSP mixtures to exclude rare alleles and unambiguously assign a two-digit HLA allele family. This gave an overall typing resolution equivalent to or greater than the split specificity level and covered all HLA-A, -B, -C, -DRBland DQB1 alleles listed in the WHO's Nomenclature for Factors of the HLA System, 2000. The Welsh Bone Marrow Donor Registry has used this strategy to HLA type over 35,000 HSC donors over 9 years. Comprehensive and accurate five-locus HLA typing allows confident and rapid identification of potential matched HSC donors for patients requiring stem cell transplantation generally without the need for typing additional loci. This allows resources to be focused directly on allele level typing of DRB1 and other loci. This strategy decreases overall donor work-up time, which is a major benefit to patients.

HLA dictionary 2004: summary of HLA-A, -B, -C, -DRB1/3/4/5, -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR, and -DQ antigens

This report presents serologic equivalents of human leukocyte antigen (HLA)-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, and -DQB1 alleles. The dictionary is an update of the one published in 2001. The data summarize equivalents obtained by the World Health Organization (WHO) Nomenclature Committee for Factors of the HLA System, the International Cell Exchange (UCLA), the National Marrow Donor Program, recent publications, and individual laboratories. This latest update of the dictionary is enhanced by the inclusion of results from studies performed during the 13th International Histocompatibility Workshop and from neural network analyses. A summary of the data as recommended serologic equivalents is presented as expert assigned types. The tables include remarks for alleles, which are or may be expressed as antigens with serologic reaction patterns that differ from the well-established HLA specificities. The equivalents provided will be useful in guiding searches for unrelated hematopoietic stem cell donors in which patients and/or potential donors are typed by either serology or DNA-based methods. The serological-DNA equivalent dictionary will also aid in typing and matching procedures for organ transplant programs whose waiting lists of potential donors and recipients are comprised of mixtures of serologic and DNA-based typings. The tables with HLA equivalents and a questionnaire for submission of serologic reaction patterns for poorly identified allelic products will be made available through the World Marrow Donor Association Web page (www.worldmarrow.org).

The HLA Dictionary 2004: a summary of HLA-A, -B, -C, -DRB1/3/4/5 and -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR and -DQ antigens

This report presents serological equivalents of HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5 and -DQB1 alleles. The dictionary is an update of that published in 2001. The data summarize equivalents obtained by the World Health Organization Nomenclature Committee for Factors of the HLA System, the International Cell Exchange (UCLA), the National Marrow Donor Program (NMDP), recent publications and individual laboratories. This latest update of the dictionary is enhanced by the inclusion of results from studies performed during the 13th International Histocompatibility Workshop and from neural network analyses. A summary of the data as recommended serological equivalents is presented as expert assigned types. The tables include remarks for alleles, which are or may be expressed as antigens with serological reaction patterns that differ from the well-established HLA specificities. The equivalents provided will be useful in guiding searches for unrelated haematopoietic stem cell donors in which patients and/or potential donors are typed by either serology or DNA-based methods. The serological DNA equivalent dictionary will also aid in typing and matching procedures for organ transplant programmes whose waiting lists of potential donors and recipients comprise mixtures of serological and DNA-based typings. The tables with HLA equivalents and a questionnaire for submission of serological reaction patterns for poorly identified allelic products will be made available through the WMDA web page (http://www.worldmarrow.org) and, in the near future, also in a searchable form on the IMGT/HLA database.

Identification of a novel allele HLA-A*1113 in a Japanese donor

Anew HLA-A*11 allele, A*1113, was identified in a healthy Japanese female. She was typed as HLA-A11?, A2, B46, B67, Cw1, Cw7 (Bw6) with unusual serological reactivity of A11, suggesting possible presence of a new A*11 allele. The novel A*1113 allele was identified by haplotypic group-specific allele amplification using A*11 allele-specific primer pairs and sequence-based typing. The A*1113 allele differs from A*11011 by one nucleotide substitution in exon 3 at position 503 (A --> G) which causes an amino acid change in the alfa2 domain at residue 144 (lysine : K --> arginine : R), thus resulting in the unusual serological reactivity.

HLA DQA1 genes generate multiple transcripts by alternative splicing and polyadenylation of the 3' untranslated region

Regulation of the human leucocyte antigen (HLA) class II genes expression is an important field in immunology, because these molecules play a crucial role in the function of the immune system. HLA DQ genes expression is a complex phenomenon regulated at both transcriptional and post-transcriptional levels. In this study, we have investigated the post-transcriptional mechanisms accounting for alleles-dependent length polymorphism of DQA1 mRNA. We have first sequenced the genomic DNA encoding the 3' untranslated region (UTR) of DQA1 *0101, *0102, *0103, *0201, *0301, *0401, and *0501 alleles. We have identified two competing splicing sites: a unique splicing donor site AG/GTA located 20 nucleotides downstream from the stop codon associated to two spliced acceptor sequences, approximately 165 and approximately 370 nucleotides downstream. In addition, three polyadenylation signals have been identified, respectively, at approximately 475, approximately 795, and approximately 855 nucleotides downstream from the stop codon. Subsequently, we have analyzed mRNAs derived from DQA1 alleles in homozygous B lymphoblastoid cell lines by reverse transcriptase-polymerase chain reaction. We show that allele-dependent length polymorphism of DQA1 mRNA-3' UTR results from a combination of differential splicing and alternative polyadenylations. Four mRNA isoforms (two spliced variant cleaved at two distinct polyadenylation sites) were detected in DQA1 *0101, *0102, and *0103 homozygous cell lines, and six mRNA species (three spliced variant cleaved at two polyadenylation-sequence signal) were generated by the other four alleles. Possible advantages for cells to generate multiple transcripts previously undetected are discussed.

Identification of two new HLA-DRB1 alleles: HLA-DRB1*1350 and DRB1*140502

Two new HLA-DRB1 alleles have been found by using high-resolution sequence-based typing. The two sequences have been officially named DRB1*1350 (HWS10001327-AY048687) and DRB1*140502 (HWS10001790-AY129430). DRB1*1350 differs from DRB1*110101 by two amino acids at positions 37 (Y-->N) and 58 (A-->E). This allele may arise from gene conversion between DRB1*110101 and DRB1*130201 or DRB1*030101, which are commonly found in Taiwan populations. The other allele, DRB1*140502, obtained from a patient with rheumatoid arthritis, differs from DRB1*140501 at codon 58 (GCC-->GCT). However, it causes no change in amino acid sequence and would therefore not have direct clinical implications.

Two novel HLA-DRB1 alleles identified using a sequence-based typing: HLA-DRB1*1443 and HLA-DRB1*1351*

Two novel HLA-DRB1 alleles, DRB1*1443 and DRB1*1351, were identified using a sequence-based typing protocol. DRB1*1443 differed from DRB1*140501 by one single-nucleotide substitution in exon-2 (codon 77, ACC-->GCC), which corresponded to an amino acid change of threonine to alanine. DRB1*1351 was identical to DRB1*1301 but differed by a single-nucleotide substitution at codon 50 (GTG-->TTG), resulting in an amino acid change of valine to leucine. Both new alleles present unique polymorphisms, which have not been seen among other DRB1 alleles and which have no known effect on peptide binding.

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.

Class I and class II MHC polymorphisms in Mexican patients with Behçet’s disease

Behçet's disease is a multi-system inflammatory disorder of unknown etiology. The disease is more prevalent in Eastern Mediterranean countries and Japan where there is a linkage to HLA-B51. Mexican Mestizos are suitable subjects for studying the role of ethnicity in the susceptibility to Behçet's disease. High-resolution HLA class I and class II typing was performed by polymerase chain reaction sequence-specific oligonucleotide (PCR-SSO) reverse dot blot and PCR-single-strand polymorphism in 32 patients with Behçet's disease and 99 healthy ethnically-matched controls. A significant increased frequency of HLA-B(*)44 (P = 0.02; OR = 2.78; CI 95% = 1.1-7.7), HLA-B(*)52 (P = 0.02; OR = 5.33; CI 95% = 1.07-29.1), and HLA-B(*)56 (P = 0.003; OR = 4.19; CI 95% = 3.37-5.21) as well as HLA-DRB1(*)01 and HLA-DRB1(*)13 (p = 0.007; OR = 3.36; CI 95% = 1.22-9.27) was found in Mexican patients with Behçet's disease when compared to controls. The low frequency of native markers in Mexican Mestizo patients with Behçet's disease suggests that genetic admixture between Eastern Mediterraneans and Orientals with Amerindians is a recent event that increased the risk of developing Behçet's disease in the Mexican population.

Variable hematopoietic graft rejection and graft-versus-host disease in MHC-matched strains of mice

MHC typing for human hematopoietic cell transplantation (HCT) from unrelated donors is currently performed by using a combination of serologic and molecular techniques. It has been determined that allelic differences in human MHC molecules, revealed by nucleotide sequencing but not by serologic typing, substantially influence graft rejection and graft-versus-host disease, two serious complications of clinical HCT. We studied transplantation of purified hematopoietic stem cells in a series of mouse strains that were matched at the MHC but had different background genes, and we observed striking differences in engraftment resistance and graft-versus-host disease severity, both factors depending on the donor-recipient strain combination. The individual mouse lines studied here were established nearly a century ago, and their MHC types were determined exclusively by serologic techniques. We considered the possibility that serologically silent MHC polymorphisms could account for our observations and, therefore, we performed DNA sequencing of the class I and II MHC alleles of our mouse strains. At each locus, exact homology was found between serologically MHC-matched strains. Our results likely extend to all serologically MHC-matched mouse strains used in modern research and highlight the profound and variable influence that non-MHC genetic determinants can have in dictating outcome after HCT.

The nature of introns 4-6 suggests reduced lineage specificity in HLA-B alleles

For most HLA-B alleles, coding sequences of the 3' part of the genes still need to be determined, and sequences of the 3' noncoding regions have yet to be studied systematically. In this study, we have determined the sequences of introns 4-6 in all HLA-B allelic groups, and computed nucleotide substitution rates and phylogenetic relationships. These sequences demonstrated an inconsistent pattern of intralineage specificity, intralineage diversity, and interlineage diversity that is best characterized by a patchwork pattern. Apart from phylogenetic studies about HLA diversity and diversification, the sequence data obtained in our study may prove valuable for haplotype-specific sequencing of the 3' part of HLA-B and for the explanation of recombination events in newly described HLA-B alleles.

T cell receptor transfection shows non-HLA-restricted recognition of nickel by CD8+ human T cells to be mediated by alphabeta T cell receptors

CD8+ T cells have been assigned a prominent role in allergic contact dermatitis, including nickel allergy; however, human nickel-reactive T cells of the CD8+ phenotype have largely escaped detailed investigation. Here we characterize two quite unusual nickel-specific cytotoxic T cell clones isolated from the peripheral blood of two nickel-sensitized patients. These clones mediate nickel-specific cytolysis of many human cell lines, independent of the expression of HLA class I, CD1, or HLA class II molecules. Lysis is mediated by the alphabeta T cell receptors and involves the perforin, but not the Fas/Fas ligand pathway. Both antigen receptors lack sequence homology to each other as well as to typical natural killer T cell receptors. A transfectant expressing the rearranged alphabeta T cell receptor derived from one of the T cell clones unequivocally demonstrates that the T cell receptor itself is necessary and sufficient to confer HLA-independent nickel specificity. The independent isolation of these clones from two individuals points to an important role of such cells in the pathology of nickel contact dermatitis.

Impact of HLA-C on acute rejection in liver transplantation

Although liver transplants show a special tolerogenic behaviour, rejection remains an important problem that involves several immunological mechanisms, some of which are unknown. Our study sought to analyze the influence of HLA-C polymorphism on short-term liver graft acceptance by HLA-C genotyping of 100 orthotopic liver transplant recipient-donor pairs. Recipients were statified according to the occurrence of acute rejection. HLA-Cw*06 allele appeared to be underrepresented among recipients without versus those with acute rejection or those in control groups. With regard to HLA-C allelic compatibility, the frequency of acute rejection or those in episodes decreased with fewer HLA-C mismatches. These findings suggest the participation of HLA-C molecules in liver graft alloresponses, involving HLA-C genotyping, as well as compatibility.