HLA Classifier

Add human leukocyte antigen (HLA) context to propel your research

Foreign antigens are presented to T cells by protein complexes called major histocompatibility complexes (MHC) that are coded for by HLA genes. HLA type plays an important role in driving T cell selection and in shaping T cell repertoires. The importance of a person’s HLA type in transplant research is well understood, as is the association of specific HLA alleles to common diseases. New research is emerging that explores the link between HLA and diseases susceptibility, response to immunotherapy, and more. By adding the HLA Classifier to samples processed using the immunoSEQ® TCRB Assay, researchers can unlock new understanding of immune repertoire dynamics in the context of HLA type.

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Accelerating discovery with the immunoSEQ HLA Classifier

Explore how HLA influences immune repertoires, disease biology, and immune-driven therapies, and discover how TCR repertoire data can be used to infer the HLA type of an individual with the new immunoSEQ HLA Classifier to accelerate discovery.

Date: Thursday, March 17th 2022
Time: 8am Los Angeles, 10am Chicago, 11am New York, 3pm London, 4pm Berlin


How does the HLA Classifier work?

We have developed the immunoSEQ HLA Classifier to infer a sample’s HLA type based on the T-cell receptor (TCR) profile. The HLA Classifier uses machine learning to provide a positive or negative call for 145 HLA genes and alleles. This unique tool is based on T-cell receptor sequencing data generated from Adaptive’s partnership with Microsoft and our Antigen Map project from ~4,000 HLA typed samples.

To develop the HLA Classifier, blood and peripheral blood mononuclear cell (PBMC) samples were TCR-sequenced to identify patterns or signals correlated with specific HLAs. The HLA Classifier compares TCR sequences found in a sample to a database of TCRs known to be associated with a certain HLA type. It runs hundreds of models to infer the HLA alleles most likely expressed in the sample.

The insights researchers gain from the HLA Classifier can enable them to study a sample’s immune repertoire in the context of HLA type and assess the role HLA plays in the susceptibility to or protection from disease.

Applications of the HLA Classifier

Understanding the T-cell repertoire in the context of HLA type has applications in many research areas, including infectious disease, autoimmune disease, and oncology. Additionally, previously sequenced blood and PBMC samples can be analyzed with the HLA Classifier to reexamine existing data.

HLA Classifier specifications

How is the data delivered in Analyzer?

HLA Classifier results are attached as a separate file to your Analyzer workspace and available for download from the Analyzer Home page.

Results pinned to Workspace.

Additional Resources

Nature Webcast - Using immunosequencing to characterize HLA and its role in disease

In this webcast, Dr. Thomas Snyder (Adaptive Biotechnologies) and Dr. Jabran Zahid (Microsoft Research) will discuss how immunosequencing and identification of public T-cell receptor responses can be used to characterize HLA type and make connections of HLA to disease biology, immune response, and immune-driven therapies.


In this blog article we explore the important role that HLA plays in the adaptive immune system and the known relationships between HLA and some common diseases.

View Article

Computational HLA Typing

In this TechNote we explore the value of HLA typing, the development of the HLA Classifier and walk through what to expect from the results.

View TechNote

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