What is human leukocyte antigen (HLA) typing?

What is HLA Typing?

HLA typing is a laboratory test that identifies the specific alleles of the human leukocyte antigen gene complex on chromosome 6p21.3, which encode major histocompatibility complex molecules that present antigens to T cells and determine immune compatibility between individuals. 1

Biological Foundation

HLA typing identifies variants within the most polymorphic gene system in the human genome, which exists to enable immune recognition of self versus non-self. 2 The HLA locus exhibits exceptional diversity driven by pathogen-mediated natural selection and displays long-range linkage disequilibrium across the entire MHC region. 1

Clinical Applications

Transplantation (Primary Use)

HLA typing is essential for matching donors and recipients in both solid organ and hematopoietic stem cell transplantation. 2

• Kidney transplantation requires high-resolution HLA genotyping (Grade 1A recommendation) for HLA-A, -B, -C, -DRB1, and -DQB1 to accurately identify donor-specific antibodies that predict antibody-mediated rejection and graft loss. 1, 3

• Hematopoietic stem cell transplantation mandates high-resolution typing of HLA-A, -B, -C, and -DRB1 for unrelated donor selection, as mismatches at these loci markedly increase mortality, acute graft-versus-host disease, and transplant complications. 1

• Heart and lung transplantation require high-resolution HLA genotyping (Grade 1B) to enable precise anti-HLA antibody specificity assessment. 1, 3

• Liver transplantation recommends high-resolution HLA-DRB1 genotyping (Grade 2C) for post-transplant donor-specific antibody assessment. 1, 3

Non-Transplant Applications

• Platelet transfusion management uses extended HLA-matching protocols for chronically transfused patients to prevent alloimmunization. 1

• Disease association studies leverage HLA typing because the HLA locus harbors more disease associations than any other genomic region, particularly for autoimmune and inflammatory disorders. 1

• Cancer immunotherapy requires precise HLA haplotyping for accurate neoantigen prediction in personalized vaccine design and for forecasting checkpoint inhibitor response. 4, 1

• Pharmacogenomics uses HLA typing to predict severe drug hypersensitivity reactions. 2

Typing Methodologies

Clinical Laboratory Methods (Gold Standard)

Sequence-specific PCR amplification combined with next-generation sequencing platforms (Illumina MiSeq, PacBio RSII) remains the gold-standard clinical method for HLA typing. 1 CAP/CLIA-regulated assays are considered robust and remain the gold standard, especially for class II loci. 4, 1

Luminex-based typing platforms provide sufficient resolution to eliminate most common ambiguities in solid organ typing, are significantly cheaper than sequencing, and are already widely implemented. 4, 1, 3

Computational Approaches

Whole-genome, whole-exome, or RNA-seq data can be used for cost-effective computational HLA typing. 4, 1 Class I typing algorithms (OptiType, Polysolver, PHLAT) achieve up to 99% concordance with clinical typing. 1 Class II typing algorithms are less reliable; clinical-grade typing remains advisable for class II loci. 4, 1

Resolution Levels

High-Resolution (Allele-Level) Typing

High-resolution typing resolves alleles at the protein-sequence level and is required in transplantation because allele-level mismatches have clinical impact comparable to antigen-level mismatches. 1 HLA alleles are named using four numeric fields (e.g., HLA-A*02:101:01:02); the first two fields are generally sufficient for peptide-MHC binding predictions. 4, 1

Why Resolution Matters

Different alleles within the same serologic family have distinct immunogenicity and vary in frequency across ethnic groups. 3 For example, HLA-B08:01 occurs in 12.5% of Caucasians versus 3.8% of African Americans; HLA-B44 includes B44:02 (≈9%) and B*44:03 (≈5%) in White individuals, which cannot be distinguished without allele-level typing. 4, 3

Technical Considerations

Sample Selection

• Peripheral blood DNA provides germline HLA alleles with high-quality genomic material and is the preferred source for most typing applications. 1

• For hematologic malignancies, skin biopsies are preferred to avoid contamination with malignant cells. 1

• Tumor DNA may be confounded by aneuploidy at HLA loci, which can impair accurate typing. 4, 1

Data Quality Requirements

• RNA-seq data often show highly variable coverage across HLA loci, leading to inconsistent typing accuracy. 4, 1

• Adequate read depth for each HLA locus must be verified to ensure confidence in typing results. 4, 1

• Employing a consensus of multiple computational tools improves confidence in HLA-typing calls. 4, 1

Critical Pitfalls to Avoid

• Do not rely on antigen-level typing alone when allele-level differences exist (e.g., B44:02 vs. B44:03), as these have distinct clinical implications. 3, 5

• Do not neglect HLA-DQ matching in kidney transplantation; both HLA-DQA1 and HLA-DQB1 chains must be assessed as heterodimers because each contributes to immunogenicity. 4, 1, 3

• Do not assume uniform HLA allele frequencies across ethnic groups, as frequencies differ markedly and influence matching probabilities. 3, 5

• Computational HLA-typing tools identify known alleles only; detection of somatic HLA mutations requires separate analytical pipelines. 4, 1