Applications Research areas
Clinical research
Obtain comprehensive and rapid analysis of clinical research samples with real-time nanopore sequencing technology. Identify and phase genetic variants with long reads, and fully characterise novel isoforms and fusion transcripts. With scalable platforms to suit all requirements, generate new insights into health and disease, from research into cancer, immunology, neuroscience, and reproductive health, to pharmacology, the microbiome, and infectious diseases, and many other areas of biomedical research.
Targeted long-read sequencing identifies missing disease-causing variation
We detected all genomic aberrations — including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences Miller, D.E. et al. Am. J. Hum. Genet. 108:8 (2021).
Oxford Nanopore sequencing
Traditional short-read technologies
Real-time data streaming
- Achieve rapid turnaround with immediate access to results
- Enrich single targets or panels during sequencing, with no additional sample prep, using adaptive sampling
- Identify microbiome composition and resistance in real time using simple EPI2ME workflows
Fixed run time with bulk data delivery
Increased time-to-result and inability to identify workflow errors until sequencing has been completed, plus additional practical complexities of handling and storing large volumes of sequence data.
Scalable and flexible
- Scale to suit your throughput needs
- Decentralise sequencing with portable Flongle and MinION
- Access flexible throughput with modular GridION and PromethION
- Perform cost-effective targeted analyses with single-use Flongle Flow Cells – from $90 each
- Use sample barcodes to run multiple samples on a single flow cell
Limited flexibility
Sample batching often required for optimal efficiency, potentially leading to long turnaround times. Benchtop devices confine sequencing to centralised locations.
Unrestricted read length (20 bp to >4 Mb)
- Resolve complex genomic regions, including structural variants (SVs) and repeats, with long reads
- Accurately phase single nucleotide variants, structural variants, and base modifications, and identify parent-of-origin effects
- Fully characterise splice variation and fusion transcripts
- Assemble high-quality genomes with fewer gaps
- Sequence short DNA fragments, such as amplicons and cell-free DNA (cfDNA)
Read length typically 50–300 bp
Short reads do not typically span entire structural variants, repeat expansions and repeat-rich regions, or transcripts of interest, potentially resulting in risk variants being overlooked, fragmented genome assemblies, and ambiguous isoform identification.
Direct, amplification-free protocols
- Detect and phase base modifications as standard – no additional prep required
- Eliminate amplification- and GC-bias
- Use amplification-free targeted sequencing approaches to detect SVs, repeats, SNVs, phasing, and methylation in a single assay
Amplification required
Amplification can introduce bias — reducing uniformity of coverage with the potential for coverage gaps — and removes base modifications, necessitating additional sample prep, sequencing runs, and expense.
White paper
The promise of nanopore sequencing for clinical and cancer research
This White paper details how real-time, scalable nanopore sequencing technology is being used to deliver novel and actionable insights across the field of biomedical research, such as identifying novel disease associations, and monitoring infectious disease outbreaks and antimicrobial resistance. Specific case studies cover the impact of tandem repeats in neurological diseases, complete genomic and epigenetic characterisation of cancer samples, preimplantation genetic testing research, HLA sequencing, and outbreak surveillance.
View more clinical research content, including workflows, infographics, publications, and videos, in our Resource centre.
Case study
The future of preimplantation genetic testing
Researchers at Columbia University Irving Medical Center, USA, demonstrated how nanopore sequencing may, in the future, support the rapid screening of embryos for chromosomal aneuploidy. Current rapid analysis techniques are limited to a subset of chromosomes, while comprehensive analysis methodologies typically take days to weeks to complete. In stark contrast, nanopore sequencing on the MinION provided comprehensive, genomewide analysis within within just a few hours of sample receipt — a timeline potentially amenable to same-day embryo transfer.
‘Sequencing times and costs range from 10 minutes and $200 per sample for ... a single sample to 2 hours and less than $50 per sample when 10 samples are multiplexed and sequenced simultaneously’
From genome-wide variant detection and phasing, to gene expression analysis and targeted panels, find comprehensive information for your research interests in our Investigations pages.
Case study
Characterising complex structural variants in disease with long nanopore sequencing reads
Danny Miller (University of Washington, USA) used nanopore sequencing to resolve complex structural variants and identify missing pathogenic variants in clinical research samples of unsolved cases of haemophilia. Nanopore whole-genome sequencing was used for the complete reconstruction of complex genomic regions, showing the future potential to shed light on unsolved haemophilia cases.
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Scalable sequencing for clinical research
From portable Flongle and MinION devices to the high-throughput benchtop GridION and PromethION platforms, scale your sequencing to match your specific clinical research requirements.
Recommended for human genome analysis
PromethION 48
Combining up to 48 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 48 delivers flexible, on-demand access to terabases of sequencing data — ideal for human genomic and transcriptomic analyses, including large cohort-based studies.
PromethION 24
Genomic and transcriptomic sequencing using up to 24 independent, high-capacity flow cells — for in-depth characterisation of large numbers of clinical research samples.
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PromethION 2 & 2 Solo
Offering two independent PromethION Flow Cells for low-cost access to high-output sequencing – ideal for smaller sample number whole-genome and transcriptome projects.
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GridION
From gene expression analysis to high-throughput targeted mutation detection, run multiple experiments on-demand using 5 independent MinION Flow Cells.
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MinION
Portable nanopore sequencing device — suitable for targeted panels, exome sequencing, and gene expression studies.
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MinION Mk1C
Integrated nanopore sequencing and analysis in a powerful handheld device — suitable for targeted analyses and gene expression studies.
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Flongle
Adapting MinION and GridION for smaller, rapid tests and analyses, on single-use flow cells; ideal for low plex targeted sequencing and library quality control.
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