HLA sequencing
[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, Belgium
Resolve and phase the entire HLA locus with nanopore reads of unrestricted length
Scale to your requirements — from portable devices to modular, on-demand benchtop sequencers
Achieve rapid sample-to-answer times with real-time sequencing
Resolve the complex HLA region
The human leukocyte antigen (HLA) region, also referred to as the major histocompatibility complex (MHC), 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 complexity and polymorphic nature of the 4 Mb region makes it challenging to resolve using short reads from legacy sequencing technology, limiting the capacity to fully resolve the region.
Nanopore sequencing reads of unrestricted length — from short to ultra-long — overcome these challenges, enabling identification of variants that could represent new biomarkers, unambiguous haplotype phasing of single-nucleotide variants (SNVs), and the potential for increased accuracy of HLA typing.
Featured content
)
New approaches for clinical research
In this white paper, discover how, through the generation of reads of unrestricted length, nanopore sequencing delivers the most comprehensive characterisation of the human genome available from a single technology.
)
Precision immunology in transplant
Find out how researchers are using nanopore technology to perform ultra-rapid, same-day reporting of HLA-related adverse drug reactions to enable precision prescribing in haematopoietic stem cell transplant patients.
Related content
)
)
)
)
GridION
A compact benchtop device designed to run and analyse up to five independently addressable MinION or Flongle Flow Cells. With adaptive sampling, perform on-device, perform target enrichment of the HLA region during sequencing — with no need for special library prep steps.
)
Adapting MinION and GridION devices to enable direct, real-time DNA sequencing, or cDNA sequencing, on smaller, single-use flow cells.
)
The only portable, real-time devices for DNA and RNA sequencing, giving complete control and creativity over when, where, and how often you sequence, regardless of application.
)
Flexible, affordable, high-output nanopore devices for every lab — in a compact, accessible form.
)
Flexible, large-scale, direct DNA and RNA sequencing devices — delivering on-demand access to terabases of data.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (20 bp to >4 Mb)
Short read length (<300 bp)
- Generate complete, high-quality genomes with fewer contigs and simplify de novo assembly
- Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
- Analyse long-range haplotypes, accurately phase single nucleotide variants (SNVs) and base modifications, and identify parent-of-origin effects
- Sequence short DNA fragments, such as amplicons and cell-free DNA (cfDNA)
- Sequence and quantify full-length transcripts to annotate genomes, fully characterise isoforms, and analyse gene expression — including at single-cell resolution
- Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
- Enhance taxonomic resolution using full-length reads of informative loci, such as the entire 16S gene
- Assembly contiguity is reduced and complex computational analyses are required to infer results
- Complex genomic regions such as SVs and repeat elements typically cannot be sequenced in single reads (e.g. transposons, gene duplications, and prophage sequences)
- Transcript analysis is limited to gene-level expression data
- Important genetic information is missed
Direct sequencing of native DNA/RNA
Amplification required
- Eliminate amplification- and GC-bias, along with read length limitations, and access genomic regions that are difficult to amplify
- Detect epigenetic modifications, such as methylation, as standard — no additional, time-consuming sample prep required
- Create cost-effective, amplification-free, targeted panels with adaptive sampling to detect SVs, repeats, SNVs, and methylation in a single assay
- Amplification is often required and can introduce bias
- Base modifications are removed, necessitating additional sample prep, sequencing runs, and expense
- Uniformity of coverage is reduced, resulting in assembly gaps
Real-time data streaming
Fixed run time with bulk data delivery
- Analyse data as it is generated for immediate access to actionable results
- Stop sequencing when sufficient data is obtained — wash and reuse flow cell
- Combine real-time data streaming with intuitive, real-time EPI2ME data analysis workflows for deeper insights
- Time to result is increased
- Workflow errors cannot be identified until it is too late
- Additional complexities of handling large volumes of bulk data
Accessible and affordable sequencing
Constrained to centralised labs
- Sequence on demand with flexible end-to-end workflows that suit your throughput needs
- Sequence at sample source, even in the most extreme or remote environments, with the portable MinION device — minimise potential sample degradation caused by storage and shipping
- Scale up with modular GridION and PromethION devices — suitable for high-output, high-throughput sequencing to generate ultra-rich data
- Perform cost-effective targeted analyses with single-use Flongle Flow Cells
- Sequence as and when needed using low-cost, independently addressable flow cells — no sample batching needed
- Use sample barcodes to multiplex samples on a single flow cell
- Bulky, expensive devices that require substantial site infrastructure — use is restricted to well-resourced, centralised locations, limiting global accessibility
- High sample batching is required for optimal efficiency, delaying time to results
Streamlined, automatable workflows
Laborious workflows
- Prepare samples in as little as 10 minutes, including multiplexing
- Use end-to-end whole-genome, metagenomic, targeted (including 16S barcoding), direct RNA and cDNA sequencing workflows
- Scale and automate your workflows to suit your sequencing needs
- Perform real-time enrichment of single targets or panels without additional wet-lab prep by using adaptive sampling
- Lengthy sample prep is required
- Long sequencing run times
- Workflow efficiency is reduced, and time to result is increased
