HLA Typing

Identify individual HLA alleles with next-generation sequencing

The human leukocyte antigen (HLA) system is a group of genes that have an important function in the human immune system. The HLA region is highly polymorphic and contains six classical HLA genes: class I with HLAA, –B and –C, and class II with HLA-DRB1, –DQB1 and –DPB1. Furthermore, the HLA region is known to be associated with more than 100 multifactorial, complex diseases, mainly with inflammatory and autoimmune pathogenesis. To find out more about the functions and complex interactions of the HLA system, next-generation sequencing (NGS)-based HLA typing can be very helpful.

The application areas of HLA typing are diverse:

  • supporting the characterization of an individual’s response to drug therapy, including pharmacogenetics
  • providing important information for immunotherapy to fight cancer
  • matching HLA regions of a donor and a recipient for a transplantation

We offer different HLA Typing products to answer your research questions.

CeGaT Is the Best Partner for Sequencing Your Project


Scalable for different sample types, quantities, and requirements


Processing according
to highest quality

Customer Service

Constant scientific supervision of all
project steps

Made in Germany

In-house processing to maintain our reliable and trusted quality

Our Commitment to You

Fast Processing

Turnaround time
≤ 15 business days

High Quality

Highest accuracy for all processes

Secure Delivery

Secure provision of sequenced data via in-house servers

Safe Storage

Safe storage of samples and data after project completion

Our Service

We provide a comprehensive and first-class project support – from selecting the appropriate product to evaluating the data. Each project is supervised by a committed scientist. You will have a contact person throughout the whole project.

Our service includes:

  • detailed project consulting
  • product selection tailored to your project
  • detailed bioinformatic evaluation of your data
  • detailed project report with information about sample quality, sequencing parameters, bioinformatic analysis, and results

Benefit from our dedicated support and accredited workflows.

Explore Our Product Portfolio for HLA Typing

Depending on the quality of the starting material we offer different HLA Typing products. Would you like to have bioinformatic analyses performed on your data in addition to the included deliverables? Each of our products can be supplemented with further services. We are happy to advise you.

HLA Classic

HLA Flex



DNA quality
High molecular weight DNA

DNA quality

HLA types
HLA class I (HLA-A, -B, and –C), and
HLA class II (HLA-DRB1, -DQB1, and -DPB1)

HLA types
HLA class I (HLA-A, -B, and –C), and
HLA class II (HLA-DRB1, -DQB1, and -DPB1)

Sequencing platform

Sequencing platform

6 Gb


Included  deliverables
Project report, files in FASTQ, TSV format

Included  deliverables
Project report, files in FASTQ, TSV format


Our HLA class I and II typing is based on our whole exome sequencing (WES). A special algorithm is used for data evaluation. You will receive the HLA typing results as TSV file, together with the previously created exome data, including demultiplexed and adapter trimmed FASTQ files.

Additional to HLA typing, we can offer further bioinformatic analysis for the exome data, of course. Please find here our bioinformatic options for additional WES data analysis.

Technical Information

HLA typing results are generated based on whole exome sequencing (WES) data with a special bioinformatic algorithm. The following loci will be analyzed:

  • HLA class I (HLA-A, -B and -C) and
  • HLA class II (HLA-DRB1, -DQB1, and -DPB1)

At CeGaT, WES is performed with paired-end sequencing (2 x 100 bp) using the Illumina sequencing platforms. If you require other sequencing parameters, please let us know! We can provide further solutions.

Our Workflow

Hier finden Sie den gesamten Prozessablauf

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Support & Offer

Support &

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Sample Receipt & Quality Control

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Library Preperation & Sequencing

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Bioinformatic Analysis & Data Delivery

Further Information about HLA Typing

During HLA typing, the different classes of the major histocompatibility complex (MHC) are determined. The HLA system is the human version of the MHC that is present in many animals. The HLA classes are located on different gene loci on chromosome 6. These genes code for cell-surface proteins that regulate the immune system. The HLA genes are highly polymorphic: Many different alleles allow the fine-tuning of the adaptive immune system. The proteins encoded by those genes are also called antigens.

HLA class I is present on all human cells carrying a nucleus. However, the highest HLA class I concentration is found on lymphocytes and macrophages. HLA class I presents peptides from the inside of the cells. These peptides are digested and broken down in the proteasome and, subsequently, presented on the cell surface. These peptides usually have a length of eight to ten amino acids. However, not only own peptides are presented: if a cell is infected with a virus, the HLA system also presents digested virus peptides on the surface of the cell. This presentation of foreign peptides attracts immune cells, such as T-lymphocytes that destroy the identified, infected cells.

In contrast to HLA class I, HLA class II presents peptides from the outside to T-lymphocytes. Foreign pathogens are captured by so-called antigen-presenting cells and phagocytosis. Thus, HLA class II is present on, e.g., B-cells, activated T-cells, or macrophages. These cells digest the pathogen and present the peptides on the HLA class II. Activated T-lymphocytes trigger the specific antibody production of corresponding B-cells.

If this well-balanced process is disturbed, diseases can spread, or novel diseases can occur. Some HLA types are connected with autoimmune disorders, such as type I diabetes, rheumatoid arthritis, systemic lupus erythematosus, or narcolepsy. HLA typing can improve and accelerate diagnosing such autoimmune disorders. But HLA typing can also have implications for cancer and its treatment. HLA typing can give valuable insights into response characterization of drug therapies, including pharmacogenetics and immunotherapies to fight cancer.

Additionally, HLA typing is a crucial step for an organ transplantation. All cells that present foreign HLA types are identified as potential threat and activate the immune system. This is very helpful in the above explained cases. However, after an organ transplantation, lots of foreign material is present in the human body. The risk of rejection of those cells, hence, the transplanted tissue, exists. The more similar the HLA antigens of donor and recipient are, the lower the risk for rejection. Thus, HLA typing is a very important step for transplantations.

HLA typing can increase the understanding of the functions and complex interactions of the HLA system and its implications on health and disease.


HLA Typing Flyer (EN)
HLA Typing Description

Contact Us

Do you have a question or are you interested in our service? Feel free to contact us. We will take care of your request as soon as possible.

Start Your Project with Us

We are happy to discuss sequencing options and to find a solution specifically tailored to your clinical study or research project.

When getting in contact, please specify sample information including starting material, number of samples, preferred library preparation option, preferred sequencing depth and required bioinformatic analysis level, if possible.