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HLA Typing with NGS

The human leukocyte antigen (HLA) is the most densely polymorphic region of the genome. HLA genes have been strongly associated with transplant rejection, autoimmune disease, vaccine pharmacogenomics (vaccinomics), cancer, and mate selection.

Previous attempts to fully characterize HLA genes have been notoriously difficult due to dense variability and sequence homology between the genes and pseudogenes. Next-generation sequencing (NGS) with Illumina sequencing by synthesis (SBS) chemistry overcomes these challenges enabling simple, high-quality analysis of the key HLA genes.

In principle, NGS is similar to Sanger (CE-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, rather than being limited to a single or a few DNA fragments. This advance enables rapid sequencing of large stretches of DNA, with the latest instruments capable of producing hundreds of gigabases of data in a single sequencing run.


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.

Multiplexing enables large numbers of loci to be sequenced simultaneously during a single experiment. To accomplish this, individual “barcode” sequences are added to each locus so they can be differentiated during the HLA data analysis.

Featured Resources

Save file HLA Typing by NGS Primer
An introduction to Illumina next-generation sequencing for HLA typing.

Save file TruSight HLA Sequencing Panel
Discover key advantages, product highlights, sample-to-report workflows, data analytics methods, chemistry, and other details.

Save file TruSight HLA v2 Whitepaper 
Results of repeated sequencing of 72 IHWG reference samples.

Save file Automating TruSight HLA
The Biomek FXP TruSight HLA automation method streamlines the workflow while providing highly reproducible and accurate HLA typing results.