The human leukocyte antigen B (HLA-B) gene is a member of the major histocompatibility complex (MHC), a region of the human genome located on chromosome 6. The MHC (also known as the human leukocyte antigen (HLA) complex) includes three subregions, designated as class I, class II and class III. Each of these subregions contains a variety of genes that mainly code for proteins involved in the immune system. HLA-B is part of the class I group, along with HLA-A and HLA-C, all three of which code for their eponymous proteins [Article:15573121]. Class II genes include HLA-DR, HLA-DP and HLA-DQ [Article:22076556], and class III genes include complement components and cytokines such as complement factor B (CFB) and members of the tumor necrosis factor (TNF) family [Articles:15573121, 14656967]. The MHC is a large region of the genome, and contains many other genes besides the ones listed above (please see Horton et al. for more details). The HLA genes are important within the field of pharmacogenetics: variations within these genes have been associated with severe drug reactions, as well as changes in how well a patient responds to a drug.

The HLA-B protein and the other class I group members are cell-surface molecules responsible for the presentation of endogenous peptides to CD8+ T-cells, and exist on almost all nucleated cells. This is in contrast to class II molecules, which display exogenous peptides to CD4+ T-cells, and are present only on antigen presenting cells (APCs) such as macrophages or dendritic cells [Articles:22076556, 18641646]. This presentation of peptides to T-cells assists in the recognition of pathogens [Article:22076556]. As a class I molecule, most of the peptides that HLA-B presents come from the normal breakdown of host cellular proteins, and are recognized by the immune system as such (i.e. "self" peptides). However, when a cell becomes infected by a pathogen, the proteins presented will be from the pathogen and recognized as foreign or "non-self". T cell antigen receptors (TCRs) on CD8+ cytotoxic T cells are responsible for this recognition, and will stimulate an immune reaction that destroys the cell [Janeway, Immunobiology, 5th edition].

Class I molecules are expressed in a codominant fashion, and humans inherit a set of HLA-A, B and C genes from each parent. Therefore, given allelic variations within these genes, up to six different class I molecules can be expressed on a cell surface. HLA-A, B and C are heterodimers consisting of an α chain, encoded by their respective genes, and a protein known as β2-microglobulin, which is encoded on chromosome 15. The α chain of HLA-B has four domains: one cytoplasmic, one transmembrane, one which binds to CD8+ cytotoxic T cells, and one which makes up a peptide-binding groove, where the presented peptide is nestled [Janeway, Immunobiology, 5th edition]. This peptide-binding region of the gene is highly polymorphic, and allelic differences between class I genes are often due to variations within this region [Article:22076556][Janeway, Immunobiology, 5th edition]. Indeed, allelic variants of class I genes can differ from one another by up to 20 amino acids. Peptides bind to the groove through interaction with specific amino acid residues, so any amino acid changes due to allelic variation may affect the peptide-binding specificity of a class I molecule [Janeway, Immunobiology, 5th edition] (class II molecules have more flexibility in peptide-binding; see Janeway). The type of extensive polymorphism seen in HLA genes allows a wide variety of peptides to be presented, and likely evolved in order to effectively combat pathogens [Janeway, Immunobiology, 5th edition]. In addition to affecting the peptides capable of being presented, allelic variants in the HLA-B gene have also been associated with susceptibility and resistance to numerous diseases, as well as adverse reactions to a wide range of pharmaceuticals. This makes HLA-B highly relevant to pharmacogenetic research.

HLA-B allele frequencies and nomenclature

Due to the highly polymorphic nature of class I genes, a large number of HLA-B alleles have been identified. Information on the frequencies of over 2800 HLA-B alleles in populations worldwide can be found at The Allele Frequency Net Database; allele frequencies for specific polymorphisms will be discussed within the individual HLA-B allele summaries. Systematic nomenclature for these alleles is invaluable given their quantity. The HLA nomenclature committee has provided a detailed nomenclature to this end, and comprehensive information on the allele naming process can be found at their website at http://hla.alleles.org. Briefly, all HLA alleles receive at least a four-digit name consisting of two sets of two digits separated by a colon, such as HLA-B*57:01. The first set of digits before the colon describes the type, typically the antigen designation used to describe the HLA alleles prior to genetic sequencing. The second set of digits indicates the specific allele, numerically ordered based on when the DNA sequence was discovered; this set of digits describes nonsynonymous substitutions only [Articles:21071412, 22378157]. This paper will only refer to the first one or two sets of digits. However, longer names, up to four sets of digits separated by colons and possibly a letter suffix, can be assigned if more detail is necessary, such as type or location of nucleotide substitution (e.g. synonymous or intronic) or resultant protein expression (e.g. null protein or cytoplasmic protein); for more information on this process, please refer to the HLA nomenclature website.

HLA-B and disease associations

A number of HLA-B alleles or allele groups have been associated with susceptibility or resistance to particular diseases. These include HLA-B*53 and resistance to malaria [Articles:1280333, 1865923], HLA-B*51 and susceptibility to the inflammatory condition Beçhet's disease [Articles:20622878, 11053265], and HLA-B*46 and increased risk of Graves' disease, an autoimmune disorder [Article:23329888]. Two particularly strong disease associations are HLA-B*57 and HIV long-term non-progression, and HLA-B*27 and ankylosing spondylitis.

HLA-B*57 and HIV long-term non-progression

Without treatment, almost all people infected with HIV will ultimately progress to acquired immunodeficiency syndrome (AIDS). However, a small percentage of patients do not advance, even long after the median progression time. These patients are referred to as long-term non-progressors or "elite controllers", and HLA-B*57 alleles, particularly *57:01 and *57:03, are highly enriched in this group of individuals [Articles:20445539, 14685052, 10694578, 21106806, 22718199, 22090105, 20205591, 23365442]. Though this association is well known, the mechanism by which it occurs remains unclear. Kosmrlj et al. used computer algorithms to predict that less than half the number of unique peptides (derived from the human proteome) bound to the HLA-B*57:01 protein as compared to HLA-B*07:01 (a non-HIV-protective form of the molecule). The authors suggested that this affected repertoire development, leading to T-cells that had been exposed to fewer self-peptides. This in turn may lead to a higher frequency of T-cells that recognize viral peptides, such as those from HIV, as well as T-cells that are more cross-reactive toward mutant epitopes. These qualities would enable the T-cells to better control the HIV infection, keeping the viral load in check and thereby making the development of AIDS unlikely [Article:20445539].

HLA-B*27 and ankylosing spondylitis

Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease, affecting mainly the axial skeleton and sacroiliac joints. It leads to inflammatory back pain, as well as other clinical features including enthesitis and anterior uveitis [Article:17448825]. Presence of HLA-B*27 leads to the greatest risk for AS, and this form of HLA-B is found in over 90% of AS patients with European ancestry. However, only 1-5% of HLA-B*27 individuals will go on to develop AS, and not all alleles of HLA-B*27 are associated with its development. While HLA-B*27:05, *27:02, *27:04 and *27:07 do confer risk, other types such as *27:06 and *27:09 do not appear to be associated with the disease [Article:16777585]. As with HIV and HLA-B*57:01, the mechanism behind this association is unknown, though several theories have attempted to explain the relationship. Several of these theories are summarized in a review by McHugh and Bowness [Article:22513152], including the arthritogenic peptide hypothesis, which suggests that HLA-B*27 binds particular peptides that give rise to a cytotoxic T-cell response, the misfolding and unfolded protein response (UPR) hypothesis, which suggests that the accumulation of abnormally folded HLA-B*27 molecules leads to an inflammatory response, and the free heavy chain and homodimer hypothesis, where AS results from the immune recognition of monomeric or dimeric ß2-microglobulin-free and peptide-free HLA-B*27 molecules [Article:22513152]. Recent GWAS analyses have identified a number of non-MHC genes associated with AS susceptibility; these genes may help explain the mechanism of AS pathogenesis. For example, multiple genes within the interleukin-23 (IL-23) proinflammatory cytokine pathway were associated with AS, indicating that this may be a core immunological pathway underlying disease development. Additionally, multiple aminopeptidase genes, such as ERAP1 and ERAP2, have been associated with AS. The protein products of these genes are involved in peptide trimming prior to HLA class I binding and presentation, suggesting that HLA-B*27 may be involved in disease development through the aberrant trimming or presentation of peptides [Articles:24504800, 23749187, 21743469, 24504793].

HLA-B pharmacogenetics

HLA-B alleles have been associated with reactions to a large number of different drugs. Some of these associations have been well studied, such as HLA-B*57:01 and abacavir hypersensitivity, HLA-B*58:01 and allopurinol-induced severe cutaneous adverse reactions (SCARs), and HLA-B*15:02 and carbamazepine-induced Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Other associations that are not as widely studied, but still show significant results include HLA-B*57:01 and flucloxacillin-induced liver injury, and HLA-B*15:02 and phenytoin-induced SJS and TEN (SJS/TEN). A list of these HLA-B alleles and their pharmacogenetic associations (along with their positive and negative predictive values, if available) can be seen in Table 1 below. For the alleles presented in this paper, there is no difference in phenotype depending on whether one or two HLA-B alleles are present, and therefore the pharmacogenetic studies discussed only consider whether an individual has the allele or not.

^{PPV, positive predictive value; NPV, negative predictive value; SCARs, severe cutaneous adverse reactions; MPE, maculopapular eruption; SJS/TEN, Stevens-Johnson Syndrome/toxic epidermal necrolysis}

Many other HLA-B alleles besides the ones mentioned above have shown associations with various drug phenotypes. A table of all the HLA-B allele and drug phenotype associations currently annotated by PharmGKB can be found under the PGx Research tab on this page. Additionally, a list of all HLA-B clinical annotations can be found under the Clinical PGx tab.

HLA-B Testing

Several options exist for determining whether a patient carries a particular HLA-B allele. The first is by direct sequencing of the gene, and assignment of a star allele after checking the sequence against known HLA-B alleles. Though this method provides high-resolution genotyping and is the most accurate, it is both time-consuming and expensive and is not widely used [Article:22378157]. An alternative and commonly used approach is genotyping, where the sequence variants known to define a particular HLA-B allele are detected using polymerase chain reaction (PCR) primers specific for each variant [Article:22378157]. Quality assurance studies done on the accuracy of HLA-B*57:01 testing using sequence-specific primer PCR (SSP-PCR) across multiple laboratories have shown very high sensitivity and specificity, indicating that laboratories using this method appear to be offering effective screening for the allele [Article:18018760]. Another method that offers cost-effective, rapid and sensitive screening for HLA-B*57:01 or HLA-B*58:01 is flow cytometry. HLA-B*57:01 and HLA-B*58:01 belong to a serological group known as HLA-B17. B17 monoclonal antibodies can be used to identify individuals who carry the HLA-B17 serotype, and these individuals can then undergo further DNA typing to determine whether they carry the *57:01 or *58:01 risk alleles. Since B17 is normally present in less than 10% of the population, assaying for presence of B17 first allows greater than 90% of a patient population to be eliminated from unnecessary HLA testing [Articles:23280011, 21501118, 16609367].

It is also possible to test for the presence of an HLA-B allele by genotyping for one more more single nucleotide polymorphirms (SNPs) nearby and in linkage disequilibrium with that allele. However, linkage disequilibrium can vary across populations, and this method may have lower accuracy [Articles:22378157, 23695185]. The HCP5 SNP rs2395029 has been suggested as a potential marker for abacavir-induced hypersensitivity, since the variant allele has shown strong linkage disequilibrium with *57:01 [Articles:18684101, 20534626, 21510768, 16998491]. However, it is not in complete concordance with *57:01 [Articles:22304574, 22913531], and individuals with the *57:01 allele but not the rs2395029 variant allele [Articles:22304574, 22913531, 20602616] as well as individuals with the rs2395029 variant allele but not the *57:01 allele [Articles:18684101, 20534626, 22304574, 22913531] have been noted. This type of incomplete concordance could result in the denial of abacavir to individuals who are not at risk for a hypersensitivity reaction, or administration of abacavir to individuals who are at risk for a hypersensitivity reaction [Articles:22378157, 20602616]. Additionally, the studies showing strong linkage between *57:01 and rs2395029 have been conducted in populations of mainly Caucasian or Hispanic descent; the strength of the linkage between the alleles has not been confirmed in large African or Asian populations [Article:22378157]. Several studies have noted that caution should be used when using rs2395029 as a surrogate marker for HLA-B*57:01 [Articles:22378157, 23592889]. However, due to the inexpensive and straightforward nature of this screening method, some laboratories do choose to perform SNP testing over allele-specific PCR [Article:22378157].

It is important to note that currently, the high level of polymorphism within the HLA genes makes HLA genotyping at a high resolution challenging [Articles:22651253, 23302098, 23714642]. Present sequencing methods can result in ambiguous typing results with an inability to resolve phase [Articles:22651253, 23302098]. Additionally, different alleles may share similar sequences within the sequenced region [Article:23714642], and defining polymorphisms may lie outside the amplified region [Articles:22651253, 23302098]. These issues may be resolved through next-generation sequencing (NGS), which allows for clonal amplification and massively parallel sequencing. These two properties provide phase information and the ability to sequence more and larger regions of genes, including intronic regions [Articles:22651253, 23302098].

A list of commercially available genetic tests for various HLA-B alleles can be found on PharmGKB; a more comprehensive list can be found at the Genetic Testing Registry. Since HLA-B expression is co-dominant, HLA-B genotyping results are either "positive", with *57:01 being present in one or both copies of the gene, or "negative", where no copies of the allele are present; there is no intermediate phenotype [Article:22378157].