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.

nanopore technology overcomes the limitations of standard short-read sequencing techniques in SV characterization

Zamora-Cánovas, A. et al. JTH, S1538-7836(23)00844-9 (2023).

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
  • Utilise intuitive EPI2ME data analysis 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

  • Scalable, automatable workflows 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

Revealing hidden genetic variants in rare disease samples

Presenting his research at the Nanopore Community Meeting 2023, Danny Miller (University of Washington, USA) highlighted the future potential of nanopore sequencing to provide rapid and comprehensive clinical genetic testing for rare paediatric diseases. As part of the 1000 Genomes Project, Danny and his team are utilising long nanopore sequencing reads to identify and characterise structural variation missed by traditional short-read-based sequencing approaches.

we know that if we use other technologies, like short-read sequencing, we miss a lot of things

Danny Miller, University of Washington, USA

Case study

Rapid DNA methylation-based classification of paediatric brain tumours

Building on previous research highlighting the potential of low-pass nanopore whole-genome sequencing to allow accurate intraoperative methylation-based profiling of brain tumours, researchers at Charité – Berlin University Medicine, Germany, demonstrated the ability to utilise otherwise discarded ultrasonic aspirator-resected tissue samples. This may, in the future, overcome the challenges of time-consuming tissue processing and limited sample material in paediatric neurooncology.

Methylation-based classification of pediatric CNS tumors based on ... discarded tissue is feasible using time- and cost-efficient nanopore sequencing

Simon, M. et al. medRxiv 23297418 (2023).

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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

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.


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