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.
Nanopore sequencing: the most comprehensive insight into cancer genomes
Without nanopore sequencing, our work wouldn’t be possible
Alberto Magi, University of Florence, Italy
Oxford Nanopore sequencing
Traditional short-read technologies
Unrestricted read length (>4 Mb shown)
- 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
- Detect and phase epigenetic modifications as standard — no additional prep required
- Eliminate amplification- and GC-bias
- Create cost-effective targeted cancer panels allowing analysis of SVs, SNVs, and DNA methylation using adaptive sampling or CRISPR/Cas9-based enrichment
Amplification required
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
Limited flexibility
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.
Streamlined workflows
- Prepare DNA samples for sequencing in as little as 10 minutes, including multiplexing
- Use whole-genome, targeted, and full-length RNA sequencing approaches
- Automate sample prep using the portable VolTRAX device
Laborious workflows
Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency and increasing turnaround times.
Accelerating cancer research through comprehensive genomic analysis
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 into the genomic causes and implications of cancer. Discover how researchers are using nanopore sequencing for comprehensive characterisation of cancer samples, delivering accurate and rapid analysis of SVs, SNVs, methylation, fusion transcripts, and splice variants — all from a single technology.
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).
The use of nanopore sequencing for epigenetic characterisation of cell-free DNA
At the NCM2022, Billy Lau (Stanford University School of Medicine, USA) presented his work using nanopore sequencing to characterise the methylation profiles of cell-free DNA (cfDNA) samples. He reported on a strategy developed by his team utilising single-molecule nanopore sequencing of cfDNA methylomes for the characterisation of cancer development.
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.
* Theoretical max output (TMO). Assumes system is run for 72 hours (or 16 hours for Flongle) at 420 bases / second. Actual output varies according to library type, run conditions, etc. TMO noted may not be available for all applications or all chemistries.
† PromethION P2 and P2 Solo devices are currently preorder, with Early Access devices expected to ship in 2022.
PromethION
PromethION Flow Cells offer the highest yield for nanopore sequencing, translating into high coverage of human and cancer genomes or the very highest read count for full-length transcripts. With a range of devices available to satisfy all throughput needs, PromethION is ideal for comprehensive whole-genome characterisation and biomarker discovery across any number of cancer samples.
The highest throughput nanopore sequencing device, capable of running up to 48 independent, high-capacity flow cells — ideal for large, population-scale cancer research studies.
Genomic and transcriptomic sequencing using up to 24 independent, high-capacity flow cells — for complete characterisation of large numbers of cancer research samples.
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.
From gene expression analysis to high-throughput targeted mutation detection, run multiple experiments on demand using five independent MinION or Flongle Flow Cells.
Portable nanopore sequencing device — suitable for low-pass whole genomes, targeted panels, exome sequencing, and gene expression studies.
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.
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.
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