Structural variation
Nanopore technology overcomes the limitations of standard short-read sequencing techniques in SV characterization
Zamora-Cánovas, A. et al. J. Thromb. Haemost. (2024)
Accurately characterise structural variants using long nanopore sequencing reads
Use amplification-free whole-genome or targeted sequencing approaches, and detect base modifications as standard
Scale to any project size, including large population-scale studies
Unlock the biology of your samples with complete SV characterisation
Structural variants (SVs) are of high importance in both normal and aberrant phenotypes; however, their detection using legacy short-read sequencing technologies is limited by their size, complexity, and position in the genome. Long and ultra-long nanopore reads can span SVs end-to-end enabling unprecedented resolution of even highly complex variants — in any genomic context. Amplification is not required, avoiding PCR bias and allowing SVs to be identified across the genome, including in repetitive or GC-rich regions, such as repeat expansions, which are inaccessible to other methods. This also enables the sequencing of intact modified bases, so that SVs and their epigenetic effects can be revealed in a single experiment.
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Resolving structural variants with long nanopore sequencing reads
Automated library preparation for short-to-long DNA fragments ensures reproducible and high-yield genomic data. This allows reliable identification of genetic aberrations, accurate phasing, high resolution of repeat regions and direct detection of DNA methylation
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Your guide to characterising structural variants
Taking you from sample to answer, this guide provides an end-to-end introduction and best-practice recommendations on calling structural variants using nanopore sequencing. Get expert tips on designing your protocol, library prep kit selection, and data analysis.
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PromethION 24
Combining up to 24 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 24 delivers flexible, on-demand access to terabases of ultra-rich sequencing data — ideal for comprehensive genomic analysis across large numbers of samples.
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Flexible, affordable, high-output nanopore devices for every lab — in a compact, accessible form.
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Flexible, large-scale, direct DNA and RNA sequencing devices — delivering on-demand access to terabases of data.
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Compact benchtop device designed to run and analyse up to five Flongle or MinION Flow Cells.
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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.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (20 bp to >4 Mb)
Short read length (50–300 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
- 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
