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.

We detected all genomic aberrations — including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences

Miller et al. Am. J. Hum. Genet. 108:8 (2021).

Technology comparison

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)

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 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 record-breaking whole-genome sequencing for rare disease identification, complete characterisation of imprinting disorders, accurate HLA sequencing, and improving blood cancer characterisation with single-cell transcriptomics.

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, genome-wide 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

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 clinical research


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.


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