Cancer research and sequencing
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'We’re really excited about this novel RNA isoform discovery that’s enabled by this platform'
Daniel Kim, University of California, Santa Cruz, USA
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 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.
Featured content
Accelerating cancer research through comprehensive genomics
Discover how cancer researchers are using Oxford Nanopore sequencing for comprehensive characterisation of cancer samples, delivering accurate and rapid analysis of SVs, SNVs, CNVs, methylation, full-length isoforms, fusion transcripts, and splice variants — all from a single technology.
Obtaining full-length isoforms from single cells
Characterisation of transcriptomic differences between individual single cells, or spatially across tissues, has provided insight into the mechanisms of cell type-specific diseases, such as cancer. Characterise isoform-level expression from full-length cDNAs at the throughput needed to analyse thousands of cells.
Recommended device for cancer research and sequencing
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PromethION 24
PromethION Flow Cells offer the highest yield for nanopore sequencing, translating into high coverage of cancer genomes and high resolution of full-length transcripts. PromethION 24 is ideal for comprehensive whole-genome characterisation and biomarker discovery across any number of cancer samples.
Featured analysis for cancer research and sequencing
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EPI2ME wf-somatic-variation
This workflow enables the analysis of somatic variation from paired tumour-normal sequence data. It processes a pair of tumour-normal BAM files, prepares quality statistics, identifies candidate SNVs and short indels using ClairS, structural variants using nanomonsv, and modified sites with Modkit.
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
