Repeat expansions
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'We have consistently shown that long-read sequencing is a reliable detector of repeat expansions'
Laß, J. et al. Mov. Disord. (2024)
Sequence complete repeat expansions, accurately determining repeat length and nucleotide composition
Explore the epigenetic profile of repeat expansions and eliminate bias with direct sequencing
Scale to your requirements — from targeted enrichment to whole-genome sequencing
Span tandem repeats in a single read
Tandem repeats (TRs) are continuously repeated bases and are a type of structural variant (SV). TR expansions are important genetic aberrations that are associated with over 50 neurodegenerative disorders. The study of such diseases requires accurate size determination of the expanded repeat, which has proven to be challenging with legacy sequencing methods such as short-read sequencing. Oxford Nanopore sequencing generates reads of unrestricted length that can span repeat expansions end to end in single reads without the need for PCR, enabling unambiguous size determination.
Featured content
Resolve challenging medically relevant genes
Long nanopore reads allow calling of copy number variants of genes with highly similar paralogs and the enumeration and motif identification of tandem repeat expansions. This poster shows how Oxford Nanopore sequencing can resolve challenging medically relevant genes.
Advancing human genomics with nanopore sequencing
Discover how researchers are utilising nanopore sequencing to enhance our understanding of human genomics by applying the benefits of nanopore technology to a variety of sequencing techniques, including whole-genome, targeted, and RNA sequencing.
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Recommended device for repeat expansion detection
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PromethION 24
Combine up to 24 independently addressable, high-capacity flow cells with a flexible, large-scale, direct DNA and RNA sequencing device for on-demand access to terabases of data — ideal for high-throughput, whole-genome sequencing with repeat expansion detection and characterisation.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (50 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
- 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
