HLA TYPING BY NGS

Introduction on HLA TYPING BY NGS:

Human Leukocyte Antigen (HLA) typing by Next-Generation Sequencing (NGS) is an advanced molecular technique that has transformed the way clinicians and researchers study immune system compatibility. The HLA system, located on chromosome 6, contains a group of highly polymorphic genes that play a vital role in distinguishing self from non-self, making them critical in organ and stem cell transplantation, autoimmune disease studies, and immunological research. Traditional HLA typing methods, such as serology or PCR-based approaches, often provide limited resolution and may not detect rare or novel alleles, leading to incomplete or ambiguous results. NGS overcomes these limitations by sequencing large stretches of DNA at high depth, enabling precise allele-level resolution and comprehensive characterization of HLA diversity.

This level of accuracy helps ensure better donor-recipient matching, reduces the risk of complications such as graft rejection or graft-versus-host disease (GVHD), and ultimately improves patient outcomes. Moreover, NGS-based HLA typing allows simultaneous processing of multiple samples, making it efficient, scalable, and suitable for both clinical practice and population-level research. By offering unmatched detail and reliability, HLA typing with NGS has become the gold standard in immunogenetics and continues to play a central role in advancing personalized medicine and transplantation success.

What is HLA typing by NGS?

HLA typing by Next-Generation Sequencing (NGS) is an advanced genetic testing method used to analyze human leukocyte antigen (HLA) genes with high precision and resolution. These genes play a key role in regulating the immune system and determining compatibility between donors and recipients in organ and stem cell transplantation. Unlike older techniques, NGS provides a comprehensive view of HLA variations, including rare or novel alleles, which helps improve donor matching, reduce transplant rejection risks, and support research in immunology, autoimmune disorders, and disease associations.

How does HLA typing by NGS testing work?

HLA typing by Next-Generation Sequencing (NGS) works by using advanced DNA sequencing technologies to generate highly detailed genetic profiles of the Human Leukocyte Antigen (HLA) genes. The process begins with collecting a biological sample, usually blood, buccal swabs, or saliva, and carefully extracting DNA. Once they isolate the DNA, laboratory specialists amplify and tag specific regions of the HLA genes to prepare sequencing libraries. They then load these libraries onto an NGS platform, which reads millions of DNA fragments in parallel and produces a large volume of sequence data. Specialized bioinformatics pipelines process this data to accurately align sequences, identify alleles, and detect even minor variations within the HLA regions.

Why is HLA typing important in stem cell transplantation?

HLA typing plays a critical role in stem cell and organ transplantation because it directly determines the level of compatibility between a donor and a recipient. Human Leukocyte Antigen (HLA) genes encode proteins that help the immune system distinguish between self and non-self cells. Since these genes are highly polymorphic, even small mismatches between donor and recipient can trigger severe immune reactions. In the case of stem cell transplantation, an HLA mismatch may cause graft-versus-host disease (GVHD), where the donor’s immune cells attack the recipient’s tissues, leading to life-threatening complications.

Why is HLA typing important in organ transplantation?

In organ transplantation, mismatched HLA types can cause the recipient’s immune system to reject the transplanted organ, reducing its survival and function.Accurate HLA typing identifies the closest possible match, lowers the risk of rejection, improves graft survival, and enhances the overall success rate of the procedure. Moreover, finding a well-matched donor through precise HLA typing not only improves clinical outcomes but also reduces the need for high doses of immunosuppressive drugs, thereby minimizing side effects and improving the patient’s quality of life. This makes HLA typing a cornerstone of safe and effective transplantation practices worldwide.

How does NGS improve the accuracy of HLA typing compared to older methods?

Next-Generation Sequencing (NGS) improves the accuracy of HLA typing by providing high-resolution and detailed analysis of genetic variations that older methods like serology or PCR-based techniques often miss. Unlike traditional approaches that may only detect broad allele groups, NGS examines the full DNA sequence of HLA genes, allowing precise identification of even rare or novel alleles. This depth of analysis minimizes errors, enhances donor-recipient matching in transplants, reduces the risk of graft rejection or graft-versus-host disease, and ensures more reliable results for both clinical and research applications.

This deeper sequencing capacity also eliminates ambiguities in allele assignments, ensuring that rare or novel alleles are detected and accurately identified. Furthermore, NGS generates large amounts of data in a single run, reducing errors that may occur due to incomplete coverage in older techniques.

Can NGS detect rare or previously unknown HLA alleles?

Yes, one of the major strengths of NGS-based HLA typing is its ability to identify rare or novel alleles that conventional methods may miss. Because NGS sequences DNA at a much deeper level, it detects genetic variations that existing databases have not previously reported. This feature is especially important in populations with high genetic diversity, where rare alleles may be more common. Detecting these alleles reduces the risk of mismatches and ensures more reliable donor-recipient compatibility in transplantation.

Which types of samples do laboratories require for HLA typing using NGS?

At My Genetic DNA Center the samples that are required is,

• Peripheral blood samples – the standard and most reliable option.
• Buccal swabs (cheek cells) – simple and non-invasive.
• Saliva samples – convenient and widely accepted.

Is NGS-based HLA typing more reliable than PCR-based or serological methods?

Yes, NGS-based HLA typing is generally more reliable than PCR-based or serological methods because it provides high-resolution results by sequencing the entire gene region rather than analyzing only limited sections. Unlike older methods, which may miss subtle variations or rare alleles, NGS offers a deeper and more comprehensive view of HLA genes, minimizing ambiguities and improving accuracy in donor-recipient matching. This advanced approach reduces the chances of errors, ensures better detection of novel alleles, and supports critical applications such as organ and stem cell transplantation where precision is essential.

Can HLA typing by NGS be used for both clinical and research purposes?

Yes, HLA typing by NGS can be effectively used for both clinical and research purposes because of its ability to deliver high-resolution and comprehensive genetic insights. In clinical practice, it plays a crucial role in organ and stem cell transplantation by ensuring accurate donor-recipient matching, reducing the risk of rejection, and improving transplant outcomes. In research, it helps scientists study genetic diversity, immune system function, and associations between HLA genes and various diseases, including autoimmune and infectious conditions. This dual application makes NGS-based HLA typing a valuable tool for advancing healthcare and scientific understanding.

What are the uses of HLA typing by NGS test?

• Organ and stem cell transplantation – Ensures accurate donor–recipient matching to reduce the risk of rejection and graft-versus-host disease (GVHD).
• Bone marrow donor selection – Identifies the closest HLA match for patients requiring bone marrow or hematopoietic stem cell transplants.
• Disease association studies – Helps researchers study the role of HLA genes in autoimmune disorders, infectious diseases, and cancer susceptibility.
• Pharmacogenomics – Detects HLA variants linked to drug responses or adverse drug reactions, improving personalized medicine approaches.
• Clinical diagnostics – Assists in identifying genetic predispositions to certain immune-mediated conditions.

Does NGS-based HLA typing provide more reliability than PCR-based or serological methods?

Yes, NGS-based HLA typing provides more reliability than PCR-based or serological methods because it offers higher resolution, greater accuracy, and the ability to detect a broader range of genetic variations. Traditional methods like PCR and serology are limited in their capacity to distinguish closely related alleles, often resulting in ambiguous or low-resolution results that may miss critical variations important for transplantation compatibility. In contrast, NGS analyzes HLA genes at the nucleotide level, providing a detailed view of even the smallest genetic differences.

This high-resolution approach reduces the chances of mismatches between donors and recipients, which is particularly crucial in stem cell and organ transplantation, where accurate typing directly impacts patient outcomes and the risk of rejection or graft-versus-host disease.

Do clinicians and researchers use HLA typing by NGS for both clinical and research purposes?

Yes, clinicians and researchers use HLA typing by Next-Generation Sequencing (NGS) for both clinical and research purposes because of its high accuracy, resolution, and ability to provide comprehensive insights into HLA genetics. In clinical practice, NGS-based HLA typing plays a crucial role in organ and stem cell transplantation, where accurate donor-recipient matching is essential to reduce the risks of graft rejection and graft-versus-host disease (GVHD). Clinicians rely on this method to identify the closest possible HLA match, ensuring better transplant outcomes and improved patient survival rates.

On the other hand, researchers use NGS-based HLA typing to study genetic diversity within populations, understand immune system functioning, and explore the association of specific HLA variants with autoimmune, infectious, and other immune-related diseases.

Why does HLA typing by NGS Test performed?

• To ensure donor–recipient compatibility in organ, bone marrow, and stem cell transplants.
• To reduce the risk of transplant rejection and complications such as graft-versus-host disease (GVHD).
• To identify rare or novel HLA alleles that may not be detected by older methods.
• To improve the accuracy of genetic matching through high-resolution sequencing.
• To support research studies exploring the role of HLA genes in immunity, diseases, and population diversity.

How accurate is HLA typing when performed using NGS testing?

HLA typing using Next-Generation Sequencing (NGS) stands as one of the most accurate methods available today, providing high-resolution analysis of HLA genes with exceptional precision. Unlike older techniques such as serology or PCR-based methods, NGS examines DNA sequences at a much deeper level and detects even minor genetic variations and rare alleles that older methods might miss.

At My Genetic DNA Center, advanced sequencing platforms and strict quality control measures ensure reliable results that meet international standards. With this technology, patients and clinicians can be confident in receiving highly accurate information, which directly supports better clinical outcomes and also contributes to research in immunogenetics and personalized medicine.

How reliable are the results of HLA typing with NGS?

The results of HLA typing with NGS are highly reliable because this technology provides high-resolution sequencing that can detect even the smallest variations in HLA genes. Unlike older methods such as serological typing or PCR-based approaches, which may miss rare alleles or provide limited resolution, NGS delivers precise and comprehensive data by analyzing the genetic sequence in detail.

At My Genetic DNA Center, the process follows strict quality control measures, including regular calibration of sequencing platforms and advanced bioinformatics pipelines, to ensure accurate alignment and variant calling. This reliability is particularly important in clinical settings such as stem cell or organ transplantation, where even minor mismatches can lead to complications like graft rejection or graft-versus-host disease (GVHD).

What is the cost of HLA typing by NGS in India?

My Genetic DNA Center sets the cost of HLA typing by NGS in India based on factors such as the required resolution, the number of loci analyzed, and whether single-locus or multi-locus typing is performed, ensuring patients receive accurate results tailored to their clinical or research needs.

Unlike My Genetic DNA Center some of the Laboratories in India set the cost of HLA typing by NGS based on the resolution required and whether they perform single-locus or multi-locus typing. On average, the price ranges between ₹10,000 and ₹30,000, though highly specialized or urgent testing may be more expensive. Some government or research-affiliated centers may offer subsidized rates for patients, while private diagnostic laboratories may charge higher fees for advanced testing packages.

How long does it usually take to get results from NGS-based HLA typing?

The turnaround time for NGS-based HLA typing typically ranges from 7 to 14 days, depending on the laboratory’s capacity, workflow, and the complexity of the test. Some high-throughput facilities with advanced sequencing platforms may provide results within a week, while urgent medical cases may qualify for expedited services that deliver results in 3 to 5 days.

At My Genetic DNA Center, the turnaround time for NGS-based HLA typing usually depends on the complexity of the test and the level of resolution required. In most cases, results are available within 7 to 10 working days, as the process involves DNA extraction, sequencing, and advanced bioinformatics analysis to ensure high accuracy and reliability.

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