Third-Generation Sequencing HLA Typing

Third-Generation Sequencing HLA Typing

1. Background Introduction

In cutting-edge fields such as CAR-T cell therapy, modification of donor cells (such as T cells) through gene editing technology is a core component. Among these, the Human Leukocyte Antigen (HLA) gene is one of the common editing targets. To ensure the precision and safety of gene editing, accurate typing and sequencing of HLA genes is crucial. Only by obtaining accurate HLA allele sequences can researchers design efficient guide RNA (gRNA) and reliably assess editing efficiency and potential off-target effects.

We understand that for most known HLA typing, the classic first-generation sequencing (Sanger sequencing) technology, with its high accuracy and mature workflow, remains the gold standard and preferred method. However, when facing novel or rare HLA alleles, or when typing results show ambiguity and uncertainty, more powerful technical means are needed to address these challenges. Therefore, we have specifically launched a high-resolution HLA typing service based on third-generation sequencing (TGS) technology as a powerful complement to our first-generation sequencing platform. This service leverages the unique advantages of long-read sequencing to completely resolve complex HLA gene regions, providing CAR-T customers and other research projects with special needs with definitive and clear sequence answers.

Figure 1. Technical Logic and Application Framework for High-Resolution HLA Genotyping in CAR-T Cell Therapy

2. Third-Generation Sequencing HLA Typing Technology Principles

Our HLA high-resolution typing pipeline employs advanced nanopore long-read sequencing technology. The core principle is to achieve direct and precise interpretation from DNA to allele typing results through single-molecule sequencing of full-length amplicons covering HLA core genes (including classic class I genes A, B, C and class II genes DRB1, DQB1, DPA1, DPB1, totaling 11 loci).

Figure 2. Third-Generation Sequencing HLA High-Resolution Typing Technology Workflow Diagram

3. Technical Innovation and Advantages

Compared with traditional technologies, our third-generation sequencing HLA typing pipeline has the following advantages:

Figure 3. HLA Gene Full-Length Coverage Analysis, Comparing Coverage Differences Between Traditional Methods and Third-Generation Sequencing Methods

4. Application Scenarios and Service Advantages

4.1 Application Scenarios

(1) CAR-T Gene Editing Effectiveness and Safety Assessment: Provide precise target sequence information for CAR-T R&D customers when editing donor HLA genes, which is the foundation for accurately assessing editing efficiency and off-target risks.

(2) Organ and Hematopoietic Stem Cell Transplantation Matching: Provide rapid and accurate HLA high-resolution matching for donors and recipients, resolve difficult or uncertain typing, and improve transplantation success rates.

(3) Disease Association Studies: In-depth research on the association between specific HLA alleles and autoimmune diseases, infectious diseases, and tumors.

(4) Pharmacogenomics: Guide personalized medication and predict drug hypersensitivity reaction risks.

(5) Marrow Bank High-Resolution Entry: Supplement and resolve cases where conventional methods cannot clearly type, meeting the high-resolution typing requirements for donor HLA loci by institutions such as the China Marrow Donor Program.

4.2 Service Advantages

(1) Leading Technology: Adopting internationally advanced third-generation sequencing platforms combined with independently optimized bioinformatics analysis workflows, ensuring the technology's forward-thinking nature and reliability.

(2) Quality Assurance: The laboratory follows a strict quality management system, ensuring that every detection step meets the highest standards and data is traceable.

(3) Professional Report Interpretation: Provide detailed and clearly formatted detection reports, equipped with a professional genetic counseling team to provide in-depth report interpretation and technical support for clinicians and researchers.

(4) Customized Services: Can provide personalized solutions from sample processing to deep data analysis according to specific customer needs.

5. Result Deliverables

We provide professional and standardized HLA high-resolution typing reports that meet clinical diagnostic and research needs. The report not only clearly displays the subject's basic information and test items but also presents high-resolution typing results at each HLA locus in an intuitive tabular format. All results strictly follow the latest database and nomenclature of the International Immunogenetics Project (IPD-IMGT/HLA) [4], and are accompanied by detailed annotations and explanations, ensuring accurate interpretation of results and reliable clinical application value.

6. Service Content and Sample Requirements

6.1 Service Content

*Service Cycle: Standard workflow 5-10 working days

6.2 Sample Requirements

6.3 Sample Information and Transport

• Information requirements: Each sample must be clearly labeled with a sample number and accompanied by a complete submission form, indicating sample type, source, and other relevant information.

• Transport guidelines: Please use sufficient dry ice (for frozen samples) or blue ice (for refrigerated samples) for transport, and select reliable courier services to ensure sample stability during transport.

Note: If samples do not meet the above requirements, it may affect data quality, extend the detection cycle, or lead to experimental failure. If you have special sample types, please be sure to contact our technical support team in advance for communication.

7. References

[1] Sino-us-diagnostics.com. (n.d.). Third-Generation Sequencing HLA Typing - A New Choice for Precision Typing. [online] Available at: [Accessed 2 Feb. 2026].

[2] Chen J., et al. (2019). High-resolution HLA genotyping using third-generation sequencing combined with targeted capture technology. Hereditas (Beijing), 41(10), pp.974-982. [online] Available at: [Accessed 2 Feb. 2026].

[3] Cobioer.com. (2024). Human Leukocyte Antigen HLA Genotyping Standards - Technical Articles. [online] Available at: https://www.cobioer.com/solution/index62.html [Accessed 2 Feb. 2026].

[4] Robinson, J., et al. (2019). The IPD-IMGT/HLA Database. Nucleic Acids Research, 48(D1), pp.D948-D955.