Nomenclature for factors of the HLA system, 1989

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 Next generation sequencing (NGS) has superseded previous methodologies of HLA typing and can generate large amounts of high-resolution sequencing data.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.

The IPD-IMGT/HLA Database

It is 24 years since the IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The database now contains over 35 000 alleles of the human Major Histocompatibility Complex (MHC) named by the WHO Nomenclature Committee for Factors of the HLA System. This complex contains the most polymorphic genes in the human genome and is now considered hyperpolymorphic. The IPD-IMGT/HLA Database provides a stable and user-friendly repository for this information. Uptake of Next Generation Sequencing technology in recent years has driven an increase in the number of alleles and the length of sequences submitted. As the size of the database has grown the traditional methods of accessing and presenting this data have been challenged, in response, we have developed a suite of tools providing an enhanced user experience to our traditional web-based users while creating new programmatic access for our bioinformatics user base. This suite of tools is powered by the IPD-API, an Application Programming Interface (API), providing scalable and flexible access to the database. The IPD-API provides a stable platform for our future development allowing us to meet the future challenges of the HLA field and needs of the community.

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.

A gene feature enumeration approach for describing HLA allele polymorphism

HLA genotyping via next generation sequencing (NGS) poses challenges for the use of HLA allele names to analyze and discuss sequence polymorphism. NGS will identify many new synonymous and non-coding HLA sequence variants. Allele names identify the types of nucleotide polymorphism that define an allele (non-synonymous, synonymous and non-coding changes), but do not describe how polymorphism is distributed among the individual features (the flanking untranslated regions, exons and introns) of a gene. Further, HLA alleles cannot be named in the absence of antigen-recognition domain (ARD) encoding exons. Here, a system for describing HLA polymorphism in terms of HLA gene features (GFs) is proposed. This system enumerates the unique nucleotide sequences for each GF in an HLA gene, and records these in a GF enumeration notation that allows both more granular dissection of allele-level HLA polymorphism and the discussion and analysis of GFs in the absence of ARD-encoding exon sequences.

Spatial pattern of adaptive and neutral genetic diversity across different biomes in the lesser anteater (Tamandua tetradactyla)

The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and activation of the adaptive immune response and are thought to be regulated by natural selection, especially due to pathogen‐driven selective pressure. In this study, we investigated the spatial distribution of MHC class IIDRB exon 2 gene diversity of the lesser anteater (Tamandua tetradactyla) across five Brazilian biomes using next‐generation sequencing and compared the MHC pattern with that of neutral markers (microsatellites). We found a noticeable high level of diversity in DRB (60 amino acid alleles in 65 individuals) and clear signatures of historical positive selection acting on this gene. Higher allelic richness and proportion of private alleles were found in rain forest biomes, especially Amazon forest, a megadiverse biome, possibly harboring greater pathogen richness as well. Neutral markers, however, showed a similar pattern to DRB, demonstrating the strength of demography as an additional force to pathogen‐driven selection in shaping MHC diversity and structure. This is the first characterization and description of diversity of a MHC gene for any member of the magna‐order Xenarthra, one of the basal lineages of placental mammals.

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/.

Genome-wide association study of aspirin-exacerbated respiratory disease in a Korean population

Aspirin-exacerbated respiratory disease (AERD) is a nonallergic clinical syndrome characterized by a severe decline in forced expiratory volume in one second (FEV1) following the ingestion of non-steroidal anti-inflammatory drugs (NSAIDs) such as aspirin. The effects of genetic variants have not fully explained all of the observed individual differences to an aspirin challenge despite previous attempts to identify AERD-related genes. In the present study, we performed genome-wide association study (GWAS) and targeted association study in Korean asthmatics to identify new genetic factors associated with AERD. A total of 685 asthmatic patients without AERD and 117 subjects with AERD were used for the GWAS of the first stage, and 996 asthmatics without AERD and 142 subjects with AERD were used for a follow-up study. A total of 702 SNPs were genotyped using the GoldenGate assay with the VeraCode microbead. GWAS revealed the top-ranked variants in 3' regions of the HLA-DPB1 gene. To investigate the detailed genetic effects of an associated region with the risk of AERD, a follow-up targeted association study with the 702 single nucleotide polymorphisms (SNPs) of 14 genes was performed on 802 Korean subjects. In a case-control analysis, HLA-DPB1 rs1042151 (Met105Val) shows the most significant association with the susceptibility of AERD (p = 5.11 × 10(-7); OR = 2.40). Moreover, rs1042151 also shows a gene dose for the percent decline of FEV1 after an aspirin challenge (p = 2.82 × 10(-7)). Our findings show that the HLA-DPB1 gene polymorphism may be the most susceptible genetic factor for the risk of AERD in Korean asthmatics and confirm the importance of HLA-DPB1 in the genetic etiology of AERD.

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.

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.

Signatures of historical demography and pathogen richness on MHC class I genes

The extreme polymorphism of MHC class I has been argued to be driven by balancing selection from pathogens, with the prediction that populations exposed to a wider variety of diseases should have higher diversity. We assembled a global database of allotype frequencies for MHC class I genes and investigated possible drivers of genetic diversity, measured in different ways. We first looked for a decline in diversity with distance from Africa (a consequence of drift during human expansions) and then investigated the link with pathogen richness once the effect of drift had been corrected for. Using heterozygosity, we recovered a clear decline in diversity from Africa and confirmed the positive relationship between genetic diversity and pathogen richness for all three classical MHC class I genes. However, when we considered a sequence-based measure of genetic diversity, the correlation with geographic distance from Africa vanished for HLA-C, and the correlations with pathogen richness for the three MHC class I genes were much weaker. HLA-C is known to consist of two functional classes of allotypes (classified with respect to the 80th residue), which interact with different KIR receptors. While this separation provided some improvement in the fit between genetic diversity and distance from Africa for one class, much clearer and consistent patterns were recovered when we used the 90th residue to separate HLA-C allotypes into two new classes. This suggests that this residue, which is also involved in the binding of KIR, might have had an important evolutionary role that has been overlooked.

The IMGT/HLA database

It is 10 years since the IMGT/HLA database was 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. Many of the genes encode proteins of the immune system and are highly polymorphic. The naming of these HLA genes and alleles, and their quality control is the responsibility of the WHO 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 this data through the website http://www.ebi.ac.uk/imgt/hla/. The first release contained 964 sequences, the most recent release 3300 sequences, with around 450 new sequences been added each year. The tools provided on the website have been updated to allow more complex alignments, which include genomic sequence data, as well as the development of tools for probe and primer design and the inclusion of data from the HLA Dictionary. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the HLA community, and the wider research and clinical communities.

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.

The IMGT/HLA and IPD databases

The IMGT/HLA database (www.ebi.ac.uk/imgt/hla) has provided a centralized repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System since 1998. Since its initial release, the database has rapidly grown in size and is recognized as the primary source of information for the study of sequences of the human major histocompatibility complex. The Immuno Polymorphism Database (IPD; www.ebi.ac.uk/ipd) is a set of specialist databases related to the study of polymorphic genes in the immune system. The 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 contains alloantigens expressed only on platelets (human platelet antigens or HPA); and IPD-ESTDAB provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines.

IMGT/HLA database--a sequence database for the human major histocompatibility complex

The IMGT/HLA Database is a specialist database for sequences of the human major histocompatibility (MHC) system. It includes all the HLA sequences officially recognised and named by the WHO Nomenclature Committee for Factors of the HLA System. The database provides users with online tools and facilities for the retrieval and analysis of these sequences. These include allele reports, alignment tools and a detailed database of all source cells. The online IMGT/HLA submission tool allows the submission of both new and confirmatory allele sequences directly to the WHO Nomenclature Committee for Factors of the HLA System. The latest version (release 1.4.1, November 1999) contains 1,015 HLA alleles from over 2,270 component sequences derived from the EMBL/GenBank/DDBJ databases. From its release in December 1998 until December 1999 the IMGT/HLA website received approximately 100,000 hits. The database currently focuses on the human major histocompatibility complex but will be used as a model system to provide specialist databases for the MHC sequences of other species.

Clonotype analysis of human alloreactive T cells: a novel approach to studying peripheral tolerance in a transplant recipient

The recognition of allo-MHC and associated peptides on the surface of graft-derived APC by host T cells (direct pathway allorecognition) plays an important role in acute rejection after organ transplantation. However, the status of the direct pathway T cells in stable long term transplants remains unclear. To detect alloreactive T cell clones in PBL and the allograft during the transplant tolerance, we utilized RT-PCR instead of functional assays, which tend to underestimate their in vivo frequencies. We established alloreactive CD4+ and CD8+ T cell clones from peripheral blood sampled during the stable tolerance phase of a patient whose graft maintained good function for 9 years, 7 without immunosuppression. We analyzed the sequence of TCR Vbeta and Valpha genes and made clonotype-specific probes that allowed us to detect each clone in peripheral blood or biopsy specimens obtained during a 1-year period before and after the rapid onset of chronic rejection. We found an unexpectedly high level of donor HLA-specific T cell clonotype mRNA in peripheral blood during the late tolerance phase. Strong signals for two CD4+ clonotypes were detected in association with focal T cell infiltrates in the biopsy. Chronic rejection was associated with a reduction in direct pathway T cell clonotype mRNA in peripheral blood and the graft. Our data are inconsistent with the hypothesis that direct pathway T cells are involved only in early acute rejection events and suggest the possibility that some such T cells may contribute to the maintenance of peripheral tolerance to an allograft.

Polymorphism and distribution of HLA-DR2 alleles and haplotypes in a Greek population

HLA-DR2 serological subtyping has indicated that the DR16 serotype appears at a higher frequency relative to the DR15 serotype in the Greek population, differing from the distribution observed in most other Caucasian groups. In this study, we have analyzed by the PCR-SSP technique a DR2-positive group of unrelated Greek individuals selected from our normal control panel for the different DRB1, DRB5, DQB1 and DQA1 DR2-associated alleles present. Six of the 50 individuals analyzed were homozygous for DR2, contributing a total of 56 haplotypes for DR2. The observed frequencies of the DR2-related DRB1 alleles were as follows: 58.9% for the DRB1*1601, 7.1% for the DRB1*1602, 25.0% for the DRB1*1501 and 7.1 % for the DRB1*1502 allele. The rare allele DRB1*1605 was detected in one heterozygous sample and its presence was definitively established by DNA sequencing. The alleles *1503, *1504, *1505, *1603 and *1604 were not detected. Three DRB5 alleles were identified: DRB5*0202 (67.8%), DRB5*0101 (25.0%) and DRB5*0102 (7.1%). Ten different DRB1/DQB1/ DQA1 DR2-associated haplotypes were defined. The most frequently observed haplotype was DRB1*1601-DQB1*0502-DQA1*0102 (relative frequency=57%) followed by DRB1*1501-DQB1*0602-DQA1*0102 (relative frequency=14.3%). In conclusion, the refined analysis of the DR2-associated DRB1 alleles in the Greek population revealed the prevalence of the DRB1*1601 allele. The rare allele DRB1*1605 was demonstrated once. A considerable variety of different DR2-related DR/DQ haplotypes was detected and the overall haplotypic frequencies in the Greek population are distributed differently compared to those reported for most other Caucasian populations.

The absence of DR51 in a DRB5-positive individual DR2ES is caused by a null allele (DRB5*0108N)

DR51, a protein encoded by the DRB5 gene, was shown to be present in almost all DR2-positive haplotypes. Exceptions were reported, some DR2-negative samples were shown to be DR51 positive and in a number of DR2-positive samples no DR51 antigen could be demonstrated. In some of them lack of the DRB5 gene was the cause of the absence of DR51 but in others the DRB5 gene was present without resulting in a detectable gene product. Many of these variants were studied in detail in previous international workshops. One of them was DR2ES from our laboratory. She is a DR15-positive DR51-negative individual of oriental origin with a clearly demonstrable DRB5*01 allele when typed by molecular techniques. To unravel the molecular mechanism responsible for the defect in expression, cDNA and DNA encoding the defective DRB5 allele were analyzed. Nucleotide sequence analysis of exon 2 showed no differences from the sequence of DRB5*0102. However, when exon 3 was examined a difference in length was noticed due to a deletion of 19 nucleotides between codon 161 and 168. The deletion caused a frameshift and a premature stopcodon resulting in a null allele. The same allele could be demonstrated in 6 other unrelated individuals of oriental origin as well as in 5 individuals from South Africa. The absence of the DR51 protein was explained by the presence of an alteration in the DRB5 allele resulting in a null allele. The allele has been officially named DRB5*0108N. This is the first description of a null allele of the DRB5 gene.

A novel, highly efficient peptide-HLA class I binding assay using unfolded heavy chain molecules: identification of HIV-1 derived peptides that bind to HLA-A*0201 and HLA-A*0301

A novel cell-free, highly automated peptide-HLA binding assay has been designed during which a mixture of unfolded recombinant HLA heavy chain molecules, beta 2-microglobulin and a fluorescent labeled standard peptide is allowed to form peptide-HLA complexes. The binding of a peptide of interest is monitored as the ability to inhibit the formation of fluorescent peptide-HLA complexes. The assay was validated using published, known HLA-A* 0201 and HLA-A* 0301 binding peptides. In addition a selected set of HIV-1LAI reverse transcriptase derived 10-mer peptides, that had been selected on the basis of HLA-A* 0201 or HLA-A* 0301 binding motifs, were tested for HLA-A* 0201/A* 0301 binding. In that set we identified 8 peptides which bound with high affinity to HLA-A* 0201 and 5 peptides which bound with high affinity to HLA-A* 0301. The major advantage of the use of denatured heavy chain is the improved economy and efficiency, as unfolded protein material is in principle easily accessible by recombinant technology.

Distribution of HLA DQ A1 alleles and genotypes in two Spanish populations (Aragon and Asturias)

HLA DQ A1 is probably one of the PCR-based genetic marker systems most widely used in actual forensic casework analyses. As accurate data about the distribution of the alleles is one of the most important prerequisites for the application in forensic biology, we studied the allele distribution in two relevant Spanish populations (Aragonese and Asturian). Results were in good agreement with the Hardy-Weinberg law in both Aragonese and Asturian populations. The power of discrimination was 0.92 in the Aragonese and 0.93 in Asturian sample. A test for homogeneity of the HLA DQ A1 population data based on alelle frequency counts for 12 European samples was performed and no significant differences were found (P = 0.831).

Role of HLA class II alleles in Korean patients with IDDM

MHC associations with IDDM in the Korean population were studied to investigate genetic susceptibility to this disorder. The frequencies of HLA-DR3, -DR4 and -DR9 were significantly higher in diabetic patients. However, the frequency of DR2 was significantly decreased in diabetic patients. DQA1*0301 and DQA1*0501 were positively and DQA1*0102 and DQA1*0201 negatively associated with IDDM. DQB1*0301 and DQB1*0601 were negatively associated with IDDM. Heterodimers DQA1*0301-DQB1*0201, DQA1*0501-DQB1*0201 and DQA1*0501-DQB1*0302 were positively associated with DQA1*0102-DQB1*0601 negatively associated with IDDM. The frequencies of DR3-DQA1*0301-DQB1*0201 and -DQA1*0501-DQB1*0201 were significantly higher in diabetic patients. The frequencies of DR4-DQA1*0301-DQB1*0201 and DR9-DQA1*0301-DQB1*0303 were significantly higher in diabetic patients. The presence of non-aspartic acid at position 57 of the DQ beta-chain was not associated with susceptibility to IDDM. However, the frequency of Arg 52 homozygotes was significantly higher in diabetic patients. These results suggest a role of the MHC molecule and also suggest racial differences in susceptibility to IDDM even within the Asian populations.

Extended HLA haplotypes among the Bari Amerindians of the Perija Range. Relationship to other tribes based on four-loci haplotype frequencies

Extended HLA haplotypes among Bari Amerindians living at the Perija Range on the limits between Colombia and Venezuela have been defined using serology for class I, electrophoresis and immuno-fixation for Bf and C4, and PCR-SSO for class II loci typing. Haplotypes were assigned based on family studies and gene frequencies were calculated using a subset of less related subjects selected from the genealogy. No rare class III variants were observed, but the characteristic low HLA diversity of isolated Amerindians populations present also in the Bari extends to Bf and C4. Thus there were only 22 different haplotypes segregating in families when nine loci were considered. All of them except three carried Bf*S, C4A*3, C4B*1. The null allele C4A*Q0 reached a frequency of 0.147 and was predominantly present in A24 Cw7 B39 DRB1*0411 haplotypes. In contrast to what has been reported using HLA alleles or class I haplotype frequencies and other isolated South American tribes, genetic distance estimates based on A-Cw-B-DR haplotype frequencies show a closer relationship between the two linguistically but geographically distant Venezuelan tribes, the Bari and the Warao, as compared to two culturally different Brazilian populations. The information reported here will be useful for identifying ancestral haplotypes in native peoples of America, for population comparison, and for discussing the differential influence of MHC haplotype diversity and population survival when similar data on other Amerindian tribes becomes available.