HLA Sequencing

Translational Genomics

High-Accuracy HLA Sequencing Streamlined

Sequencing the HLA region can provide critical insight into immune disorders. Achieving high-resolution human leukocyte antigen (HLA) typing results with conventional methods requires multiple assays, systems, and analysis programs.

HLA typing by next-generation sequencing (NGS) generates unambiguous, phase-resolved HLA typing results using a single assay, system, and analysis program.

Scientist pipetting in lab

Benefits of NGS-Based HLA Analysis

The HLA region is the most densely polymorphic region of the genome. Sequencing HLA genes used to be notoriously difficult due to high levels of sequence homology between HLA genes and pseudogenes, dense variability, and poor characterization of the thousands of HLA alleles in the population.

NGS with Illumina sequencing by synthesis (SBS) chemistry overcomes these challenges, enabling simple, high-quality analysis of the key HLA genes. Highly accurate and robust Illumina SBS chemistry is a widely adopted NGS technology worldwide.

Application of NGS to HLA Analysis

In principle, NGS is similar to Sanger (capillary electrophoresis-based) sequencing. The bases of a DNA fragment are identified sequentially from signals emitted as each fragment is resynthesized from a DNA template strand. NGS scales up this process; millions of reactions occur in a massively parallel fashion. This advance enables rapid sequencing of large stretches of DNA such as the HLA region.

Learn More About NGS Technology

Phase-Resolved HLA Sequence Analysis

Illumina NGS technology supports paired-end sequencing, a unique feature that is crucial for successful, unambiguous HLA typing. Sequencing the ends of the library DNA fragments generates high-quality base calls. The physical link between the 2 reads (originating from the same clonally amplified library DNA fragment) allows association of variants found in each read pair. The distance between the paired reads varies as a result of the random library fragment generation process, allowing the direct resolution of the phase of 2 variants.

Learn More About Paired-End Sequencing

Featured HLA Sequencing Research

Tumor-Specific HLA Ligands
Precision Immunotherapies Using Tumor-Specific HLA Ligands

RNA-Seq and HLA typing are increasing the power and efficiency of a target discovery platform.

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Targeted DNA Analysis
HLA Genetics & Autoimmune Disease

Researchers query the genome with NGS and perform HLA genotyping to identify novel risk loci for immune-mediated disease.

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DNA sequencing
Exploring HLA Diversity in Brazil

Drawing upon the genetic diversity of Brazilians, scientists develop an HLA variation database.

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Gain Insight into Immunological Diseases

NGS and microarray solutions enable researchers to investigate potential autoimmune disease mechanisms, the immune repertoire, tumor immunogenicity, and the functional consequences of immune-related genetic variation.

Learn More About Immunogenomics

immuno-oncology research

Advantages of Multiplexing

Multiplexing enables large numbers of loci to be sequenced simultaneously during a single experiment. Individual “barcode” sequences are added to each locus so they can be differentiated during HLA sequencing data analysis.

Learn More About Multiplex Sequencing

Sample-to-Report HLA Typing

The TruSight HLA v2 Sequencing Panel (originally developed by Illumina and now available from CareDx) enables phase-resolved, sample-to-report HLA typing for 11 loci in a single assay, with a single workflow, on a single instrument, for dozens of samples simultaneously. Gone are the days of resolving ambiguities for every sample at every locus; TruSight HLA delivers an ultra-high–resolution typing result the first time.

View CareDx TruSight HLA page

HLA Sample to Report

Featured Sequencing Instruments

  • MiniSeq System: With a low purchase price and cost-efficiency even for low sample numbers, the MiniSeq System enables a broad range of targeted DNA and RNA applications.
  • MiSeq System: Access focused applications such as targeted resequencing, metagenomics, targeted gene expression profiling, and more.

See All Sequencers

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Additional Resources

Multiomics in Clinical Research

Multiomic approaches enable a more comprehensive understanding of samples and can be used to improve the quality and pace of clinical research.

Illumina Sequencing by Synthesis
Illumina Sequencing by Synthesis

Illumina SBS chemistry has revolutionized the study of genomics. See SBS chemistry in action.

*Data calculations on file. Illumina, Inc., 2015