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, multiple techniques are often used to identify and analyse different forms of cancer. Combining the facility to generate long sequencing reads (up to 4 Mb) that can span complex genomic regions, together with integrated base modification detection and real-time results, nanopore sequencing offers a complete, streamlined, and rapid solution for complete characterisation of cancer samples.
Robust methylation-based classification of brain tumors using nanopore sequencing
nanopore sequencing allows robust and rapid methylation-based classification across the full spectrum of brain tumors Kuschel et al. MedRxiv 21252627 (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 circulating tumour DNA and tissue 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
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 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 using high-throughput GridION and PromethION devices
- Sequence as and when required, 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 complementary 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.
Characterising structural variants in acute myeloid leukaemia
The genetic aberrations underlying a large proportion (49%) of acute myeloid leukaemia (AML) patients cannot be characterised using standard genetic techniques. Touati Benoukraf and colleagues from Memorial University of Newfoundland, Canada, propose that these ‘missing’ aberrations may be structural variants, which are challenging to resolve using traditional short-read sequencing technologies. To test this hypothesis the team utilised long nanopore sequencing reads, combined with their in-house developed SV detection tool NanoVar, to analyse a number of AML and ‘normal’ samples. At just 4–8% genome coverage, the researchers were able to accurately detect novel AML-specific SVs, which may offer potential future use as disease-specific biomarkers.
‘12 Gb of third-generation sequencing data (4x coverage) produced a more comprehensive SV detection outcome than 160 Gb of second-generation sequencing data (53x coverage)’Tham, C.Y. et al. Genome Biol. 21(1):56 (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
From gene expression analysis to high-throughput targeted mutation detection, run multiple experiments on-demand using 5 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