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Cancer research and sequencing

'We’re really excited about this novel RNA isoform discovery that’s enabled by this platform'

Daniel Kim, University of California, Santa Cruz, USA

  • Discover novel cancer biomarkers and identify known signatures with the most comprehensive genomics platform

  • Detect SVs, SNVs, and CNVs at the haplotype level and resolve full-length RNA isoforms with any-length reads

  • Simultaneously detect epigenetic base modifications by directly sequencing native DNA/RNA

Reveal more cancer biology with ultra-rich Oxford Nanopore sequencing data

The genetic underpinnings of cancer are diverse and many types of genomic aberration — from single nucleotide variants (SNVs) to structural variants (SVs), copy number variants (CNVs), fusion transcripts, and epigenetic modifications (e.g. DNA/RNA methylation) — can cause, contribute to, or indicate disease. As a result, researchers traditionally relied on multiple techniques to identify and analyse different facets of cancer.

Now, with Oxford Nanopore technology, researchers are going beyond next-generation sequencing (NGS), generating sequencing reads of any length, including ultra-long reads (>4 Mb achieved) that can span complex genomic regions. This, combined with integrated base modification detection and real-time results, means that nanopore oncology sequencing delivers a streamlined and rapid solution for complete characterisation of cancer and tumour samples.

hereditary cancer workflow diagram

Hereditary Cancer Panel

The Oxford Nanopore Hereditary Cancer Panel is a comprehensive sequencing assay targeting 258 full-length genes — covering exons, introns, and promoters — linked to inherited cancer risk. The panel uses adaptive sampling: a fast and flexible on-sequencer target enrichment methodology. No lengthy library preparation, baits, or primers required.

Technology comparison

Oxford Nanopore sequencing

Legacy short-read sequencing

    • 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
    • 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
    • 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
    • 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
    • Lengthy sample prep is required
    • Long sequencing run times
    • Workflow efficiency is reduced, and time to result is increased

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