HLA sequencing

The human leukocyte antigen (HLA) region, also referred to as the major histocompatibility complex (MHC), spans over 4 Mb on chromosome 6 and plays a central role in normal immune functions, autoimmune diseases, and transplantation. Studying the HLA locus is essential to uncovering the mechanisms behind these processes; however, the HLA region presents many difficulties owing to its complexity and polymorphic nature. The ability to span large portions of the HLA region, if not the entire locus, with long nanopore reads, offers a promising solution.

  • Resolve and phase the entire HLA locus with long and ultra-long nanopore reads
  • Scale to your requirements — from portable sequencing devices to modular, on-demand benchtop sequencers
  • Achieve rapid sample-to-answer times with real-time sequencing

Importance of the HLA system

Transplantation is the best treatment option for many types of end-stage diseases, improving both the quality and length of life. Underpinning the success of organ or bone marrow transplantation is HLA typing, which enables HLA matching of donors and recipients. Insufficient matching between donor and recipient antigens can result in fatal complications, such as organ rejection or graft-versus-host disease (GvHD).

The HLA region is a highly polymorphic region located on chromosome 6. Typically, the epitopes with high antigenicity are coded for in exons 2 (HLA class I and II) and 3 (HLA class I) of the HLA genes — these are the protein binding elements of the major histocompatibility complex (MHC) (Figure 1). HLA alleles are defined by the single nucleotide polymorphism (SNP) and indel combinations within single phased sequences, and specific nomenclature is used to define alleles. Analysing these variants forms the foundations of high-resolution typing and enhances the chances of successful transplantation.

Figure 1. MHC class II molecule: The α1 and β1 subunits of the protein binding domain are encoded for by exon 2 of their respective genes.

Figure 2: The large number of SNPs seen here when read mapping three human reference samples to the GRChH38 reference genome highlights the polymorphic nature of the HLA genes, with HLA-A shown as an example. Sequenced from 3 reference samples on a single MinION Flow Cell.

Resolving the HLA

Resolving the HLA region

In recent years, next-generation sequencing (NGS), mainly based on short-read sequencing technologies, has superseded traditional HLA typing methods, offering improved throughput and resolution, plus reduced turnaround times. However, such methods succumb to the inherent limitations of short reads, which often align ambiguously to HLA alleles and make phasing of distant variants challenging.

The long sequencing reads that can be generated on Oxford Nanopore devices have been shown to overcome the associated issues of short-read sequencing and increase the accuracy of HLA typing. Long nanopore reads, capable of spanning the entire HLA region, transforms variant detection by readily linking together adjacent variants, enabling unambiguous phasing of SNVs to a respective haplotype. An efficient method for phased determination of HLA alleles will likely aid in the discovery of additional markers of importance that will improve transplantation success. Furthermore, using long nanopore reads, variants can be called within regulatory regions, and these have the potential to influence gene expression.

Find out more in the HLA sequencing poster
Case study

Ultra-rapid, high-resolution HLA class I typing for pharmacogenetic testing

HLA genes have been shown to be involved in hypersensitivity to many drugs, with specific HLA class I alleles being most frequently implicated. In Thailand, HLA genotyping is routinely performed prior to the administration of prescription drugs; however, existing PCR-based genotyping assays often lack resolution and accuracy. To overcome these challenges, Anukul et al. utilised nanopore sequencing to deliver cost-effective and highly accurate (three- to four-field), same-day HLA typing of twenty clinical research samples.

This work demonstrates the ability of transposase-based [nanopore] sequencing to report 3-field HLA alleles and its potential for race- and population-independent testing at considerably decreased time and cost

Anukul, N. et al. Front. Genet. 14, 1213457 (2023).

MinION Mk1B image

[Nanopore sequencing] ... allows us also to do the typing to the same level as we could with next generation sequencing, but we could do it faster, our sample prep was easier and it was much more cost efficient.

Steven Verbruggen, OHMX.bio

Case study

Characterising the HLA region with PCR-free targeted nanopore sequencing

The HLA region is highly variable; accurate, phased HLA genotyping is needed to ensure the success of organ transplantation. Short-read methods for HLA typing suffer from PCR bias and phasing is difficult with short reads. These problems are overcome with PCR-free long nanopore sequencing reads. At London Calling 2022, Steven Verbruggen (OHMX.bio, Ghent) discussed his work using PCR-free targeted nanopore sequencing for HLA typing. Using adaptive sampling, which negates the need for any extra lab-based steps as enrichment is performed in real-time during sequencing, Steven achieved 10–20x enrichment of the HLA region. When using Cas9 sequencing, up to 30–40x enrichment was achieved; enough signal for high-resolution HLA typing. Steven concluded that HLA typing with nanopore sequencing is cost efficient, easy, and provides detailed results faster than any alternative technologies.


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