HLA Tissue Typing: Introducing High-Resolution Typing with Next-Generation Sequencing (NGS)

PATHCHAT Edition No. 82
Published: 2023
Please contact your local Ampath pathologist for more information.

Authors:

• Dr. P. Swanepoel
• Dr. C. Sedumedi
• Dr. H. Ranchod

Introduction to the Human Leukocyte Antigen (HLA) Molecule

✅ What is HLA?

• The major histocompatibility complex (MHC) genes are located on the short arm of chromosome 6.
• They encode cell surface markers critical for immune system function.
• The human MHC is synonymous with the human leukocyte antigen (HLA) complex.

✅ Classes of HLA Molecules:

1. MHC Class I:
   • Expressed on all nucleated cells and platelets.
   • Includes HLA-A, HLA-B, and HLA-C.
2. MHC Class II:
   • Expressed on antigen-presenting cells of the immune system.
   • Includes HLA-DQ, HLA-DR, and HLA-DP.

✅ Role of HLA in Immunity:

• Presents proteins (self and non-self) to T-lymphocytes.
• HLA genes are highly polymorphic, contributing to genetic diversity in populations.

📌 HLA molecules are essential for immune function and play a key role in transplantation, disease susceptibility, and drug reactions.

Indications for HLA Typing

✅ Primary Uses of HLA Typing:

• Transplant medicine (solid organ and stem cell transplants).
• Disease associations with specific HLA alleles.
• Pharmacogenomics (e.g., predicting drug hypersensitivity reactions).
• Bone marrow and tissue registries.
• Immunotherapy and vaccine response research.

📌 HLA typing is critical for matching organ and stem cell donors with recipients to prevent rejection or graft-versus-host disease.

HLA Typing Methods & the Advantages of NGS

✅ HLA Typing Techniques:

1. Serological Methods:
   • Older approach with limited resolution.
   • Can only detect broad antigen groups.
2. Polymerase Chain Reaction (PCR)-Based Methods:
   • Higher specificity than serology.
   • Identifies more allelic variations.
3. Next-Generation Sequencing (NGS) (Gold Standard):
   • Detects full-length HLA genes, including introns and untranslated regions.
   • Provides high-resolution typing, reducing ambiguity in donor-recipient matching.
   • Simultaneously sequences multiple HLA loci in a single assay.

✅ HLA Loci Reported Using NGS:

• HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1.

📌 NGS-based HLA typing ensures the highest accuracy in tissue matching, reducing the risk of transplant rejection.

Key Information on Ampath’s HLA Typing Test

✅ Test Details:

• Sample Type: 1 EDTA tube.
• Mnemonic for Test Request: HLATYPE.
• Turnaround Time: ~6 weeks.

📌 Ampath uses the latest NGS technology to provide high-resolution HLA typing for transplants and clinical applications.

HLA Nomenclature & Allele Naming System

✅ Understanding HLA Naming Convention:

• HLA alleles are named using a standardized format established by the WHO Nomenclature Committee.
• Each allele includes a gene name, followed by up to four sets of digits separated by colons.

✅ Structure of an HLA Allele Name:

• Example: HLA-A02:101:01:02N
  • HLA Prefix: "HLA" followed by the gene name (e.g., HLA-A).
  • First Field: Major allele group (e.g., 02).
  • Second Field: Specific HLA protein (e.g., 101).
  • Third Field: Synonymous coding-region variation (e.g., 01).
  • Fourth Field: Non-coding region variation (e.g., 02).
  • Suffix (e.g., "N") indicates changes in protein expression.

📌 HLA nomenclature is continually updated as new alleles are discovered.

Advantages of NGS-Based HLA Typing

✅ Why Choose NGS for HLA Typing?

• Increased throughput (simultaneous sequencing of multiple loci).
• High-resolution typing (up to eight digits/four fields).
• Improved accuracy and specificity.
• Reduced genotyping ambiguity.
• More cost-effective than previous methods.

📌 NGS provides the most precise and comprehensive HLA typing available today.

HLA Disease Associations

✅ Diseases Linked to Specific HLA Alleles:

1. Coeliac Disease: HLA-DQ2 and HLA-DQ8.
2. Ankylosing Spondylitis: HLA-B27.
3. Abacavir Hypersensitivity: HLA-B57:01.
4. Behçet Syndrome: HLA-B51.
5. Other Disease Associations: Various HLA loci linked to autoimmune and inflammatory conditions.

📌 HLA testing can help assess genetic predisposition to certain diseases but is not a diagnostic criterion.

HLA Typing Test Offerings at Ampath

✅ HLA Disease Association Tests:

• Coeliac Disease: HLA-DQ2 and DQ8 (HLADQ28).
• Ankylosing Spondylitis: HLA-B27 (HLAP).
• Abacavir Hypersensitivity: HLA-B57:01 (HLAB5701).
• Behçet Syndrome: HLA-B51 (HLA51).
• Other Diseases: Custom HLA typing available upon request (HLADIS).

📌 For personalized HLA testing, contact the Ampath Next-Generation Sequencing Laboratory.

Key Takeaways for Clinicians & Researchers

✅ HLA typing is essential for transplantation, disease association studies, and pharmacogenomics.
✅ NGS-based HLA typing provides high-resolution, accurate, and comprehensive genetic profiling.
✅ Ampath offers a full range of HLA typing services, including disease association testing.
✅ HLA nomenclature is complex, but standard naming conventions ensure clarity in genetic interpretation.
✅ NGS improves donor-recipient matching, reducing transplant rejection risk.

📌 For HLA typing queries, contact the Ampath NGS Laboratory at 012 678 0670 or email ngs@ampath.co.za.