Applications Research areas
Cancer research and sequencing
The genetic underpinnings of cancer are diverse and many types of genomic aberration — from SNVs to SVs, 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 forms of cancer. Now, through the facility to generate sequencing reads of any length, including ultra-long reads in excess of 4 Mb that can span complex genomic regions, combined with integrated base modification detection and real-time results, nanopore sequencing delivers a streamlined and rapid solution for complete characterisation of cancer samples.
Intraoperative DNA methylation classification of brain tumors impacts neurosurgical strategy
low-pass whole-genome nanopore sequencing can be used to generate DNA methylation profiles of a tumor biopsy that is sufficient for accurate classification in less than 2 h Djirackor, L. et al. Neurooncol Adv. 3(1):vdab149 (2021).
Oxford Nanopore sequencing
Traditional short-read technologies
Unrestricted read length (>4 Mb achieved)
- Comprehensively identify genomic aberrations, including those in complex and repetitive regions, from blood, tissue (inc. FFPE), and circulating tumour samples
- Accurately identify and phase single nucleotide variants, structural variants, and base modifications in a single sequencing assay
- Fully characterise splice variation and fusion transcripts — up to single-cell resolution
Read length typically 50–300 bp
Short reads do not typically span entire structural variants, repeat-rich regions, or full-length transcripts — requiring the use of complex computational analyses to infer results rather than direct identification. As a result, many important disease variants may be missed.
Direct, amplification-free protocols
Amplification can introduce bias — reducing uniformity of coverage with the potential for coverage gaps — and removes base modifications (e.g. DNA methylation) that have been shown to be associated with cancer risk, progression, and treatment outcomes, necessitating additional sample prep, sequencing runs, and expense.
Real-time data streaming
- Analyse data as it is generated for immediate access to results
- Perform flexible, on-device enrichment of single targets or panels, with no additional sample prep, using adaptive sampling
- Stop sequencing when sufficient data generated — wash and reuse flow cell
Fixed run time with bulk data delivery
Increased time-to-result and inability to identify workflow errors until it’s too late, plus additional practical complexities of handling large volumes of sequence data.
Flexible and on-demand
- Scale to suit your cancer sequencing requirements
- Get started with MinION at just $1,000, including flow cells and sequencing reagents
- Cost-effectively run targeted cancer panels using Flongle Flow Cells at $90 each
- Perform comprehensive whole-genome or transcriptome analyses and scale-up sample throughput with GridION and PromethION devices
- Sequence as and when required using low-cost, independently addressable flow cells — no sample batching needed
Sample batching often required for optimal efficiency, potentially leading to long turnaround times. Traditional high-throughput benchtop sequencing devices require significant infrastructure requirements and expense — confining their use to well-resourced, centralised locations.
Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency and increasing turnaround times.
Advancing clinical and cancer research with nanopore sequencing
The facility to generate sequencing reads of any length — from short to in excess of 4 Mb — combined with simultaneous base modification identification (e.g. DNA or RNA methylation) and real-time analysis is providing new and actionable insights across the fields of biomedical and cancer research. Discover how researchers are utilising nanopore sequencing for rapid and comprehensive characterisation of SVs, SNVs, fusion transcripts, and splice variants for a range diseases and samples.
Get more cancer research content in our Resource centre, including videos and publications on analysing cell-free DNA (cfDNA) from liquid biopsies.
Comprehensive structural variation detection in tumour genomes
Structural variants (SVs) are known to play an important role in cancer initiation, progression, and prognosis. However, our understanding of SVs has, until recently, been restricted to short-read technologies, which have limited facility to resolve these variants. Recognising the limitations of short-read sequencing for SV detection, Thibodeau et al. investigated the utility of nanopore technology to resolve germline SVs in cancer risk genes. The team performed nanopore sequencing on the PromethION for 13 samples for which short-read technology had proven ineffectual. Long nanopore reads enabled confirmation of the suspected SVs and resolution of SVs that could not be delineated using short reads. Nanopore sequencing revealed that, in three cases, an inverted duplication had been miscalled using short-read sequencing, and this had led to an incorrect pathogenic variant call.
‘long-read sequencing can improve the validation, resolution, and classification of germline SVs.’Thibodeau et al. Genet Med. 22(11):1892-1897 (2020).
Complete characterisation of targeted regions with adaptive sampling
Tumours of the central nervous system (CNS) are some of the most difficult to treat, with extensive morphological and molecular heterogeneity, as evidenced by the WHO 2021 classification criteria, which incorporates SNVs, CNVs, and methylation status. According to Areeba Patel, of the German Cancer Research Center (DKZF), the current technology for methylation classification takes approximately 22 days, partially caused by the requirement to batch samples to minimise analysis costs. To combat these challenges, Areeba assessed the unique potential of Oxford Nanopore’s on-device adaptive sampling technique for cost-effective, real-time enrichment of gene panels and CpG sites associated with neuropathology. The end-to-end nanopore sequencing workflow, termed Rapid-CNS2, provided ‘much higher resolution’ when compared with traditional panel sequencing approaches, while the methylation profiles were comparable to ‘gold standard’ array approaches.
‘RAPID-CNS2 provides a swift and highly flexible alternative to conventional NGS and array-based methods for SNV/InDel analysis, detection of copy number alterations, target gene methylation analysis (e.g. MGMT) and methylation-based classification. The turnaround time of ∼5 days for this proof-of-concept study can be further shortened to <24h…’Patel et al. Acta Neuropathol. (2022).
Full-length analysis of single-cell transcripts
Single-cell transcriptome sequencing is a powerful tool for high-resolution analysis of gene expression in individual cells. However, traditional high-throughput approaches only allow sequencing of a small region at one end of the transcript. As a result, information crucial for an in-depth understanding of cell-to-cell heterogeneity on splicing, chimeric transcripts, and sequence diversity (i.e. SNPs, RNA editing, imprinting) is lost. To overcome this, Lebrigand et al. developed ScNaUmi-seq, a novel workflow that leverages the long reads and high yields delivered by nanopore sequencing to accurately analyse full-length transcripts from single cells.
‘ScNaUmi-seq can be easily plugged into standard single-cell sequencing workflows and should facilitate high throughput single-cell studies on RNA splicing, editing, and imprinting. We anticipate its usefulness in many biological and medical applications, from cell biology and development to clinical analyses of tumor heterogeneity.’Lebrigand et al. Nat Commun. 11(1):4025 (2020).
Scalable sequencing for cancer research
Nanopore sequencing is uniquely scalable — from portable Flongle and MinION devices to the high-throughput benchtop GridION and PromethION platforms, there’s a nanopore sequencing device to suit your specific cancer research requirements.
Genomic and transcriptomic sequencing using up to 24 independent, high-capacity flow cells — for complete characterisation of large numbers of cancer research samples.View product
PromethION 2 & 2 Solo
Offering two independent PromethION Flow Cells for low-cost access to high-output sequencing – ideal for smaller sample number cancer genome and transcriptome projects. Available to preorder now.View product
From gene expression analysis to high-throughput targeted mutation detection, run multiple experiments on-demand using five independent MinION or Flongle Flow Cells.View product
Portable nanopore sequencing device — suitable for low-pass whole genomes, targeted panels, exome sequencing, and gene expression studies.View product
The all-in-one sequencer. Get all the benefits of the original MinION device but with integrated high-resolution touchscreen, integrated compute, and complete connectivity.View product
Adapting MinION and GridION for smaller, rapid tests and analyses, on single-use flow cells; ideal for rapid, low-plex, low-cost targeted cancer panels and library quality control.View product
Automated sample extraction and library preparation.View product