Multiomic studies utilise multiple omics methods, including genomics, transcriptomics, epigenomics, and proteomics, to gain a more comprehensive understanding of complex biology in health and disease. Combining various omics data types empowers researchers to create comprehensive disease models and unravel the myriad of interactions underlying disease mechanisms.

Legacy multiomics approaches require multiple assays, platforms, and data analyses, resulting in complex and time-consuming workflows. Now, nanopore sequencing provides the power to revolutionise your multiomic studies — from single-cell, to bulk, to targeted analysis — with streamlined workflows on a single platform.

  • Get genomic or transcriptomic and methylation data in a single assay through direct sequencing of native DNA or RNA
  • Unrestricted read lengths enable you to cover all bases, from whole genome to targeted panels
  • Explore isoforms, alternative splicing, and genotypes with single-cell and spatial resolution

Reveal more biology in a single assay

With traditional techniques, informative multiomics studies can feel as complex as the biology you are trying to uncover. What if you could get ultra-rich data — SNVs, complex SVs, CNVs, STRs, haplotyping, methylation (6mA, 5mC, and 5hmC), and RNA isoforms — from a single platform?

Nanopore sequencing enables genomic, epigenomic, and transcriptomic — including single-cell and spatial — analysis at any read length, empowering researchers to delve into complex questions and unlock transformative biological discoveries, revealing new biomolecule-disease connections, relevant signaling pathways, and precise disease biomarkers.

Ultra-rich multiomic sequencing data

Figure 1. The power of ultra-rich data. Nanopore multiomic sequencing simplifies genomic and epigenomic analysis through direct sequencing of native DNA. Methylation analysis can be activated by a single mouse click, enabling epigenomic information to be provided alongside truly comprehensive genomic data — including complex variants and phasing information — only available through long reads.

Oxford Nanopore multiomics toolkit

Figure 2. Nanopore multiomic sequencing. Advances in accuracy and output, combined with end-to-end workflows, make PromethION devices ideal for multiomics studies.

A unique toolkit for deciphering complex biology

Oxford Nanopore provides the only platform capable of direct DNA and RNA sequencing for the analysis of native nucleic acids, including base modifications (e.g. methylation). Combined with adaptive sampling — a unique on-device target enrichment methodology — and single-cell and spatial workflows, nanopore multiomic sequencing provides a cutting-edge toolkit to deliver novel insights, faster.

One platform — comprehensive multiomic analysis

Case study

Ultra-rich nanopore data offers unprecedented insights into the transcriptomes of single cells

Recent improvements in nanopore sequencing chemistries, basecalling accuracy and bioinformatic tools have enabled single-cell long read sequencing, which can deliver unprecedented insights into cell type-specific transcriptional diversity.

Byrne et al. bioRxiv (2023).

Byrne et al. developed a novel hybridisation capture method that utilises long nanopore sequencing reads to expand upon the capabilities of single-cell RNA-Seq — without the requirement for unique molecular identifier (UMI) or cell barcode identification using paired short reads. Analysis of ovarian cancer research samples revealed transcriptional complexities missed by short-read sequencing technologies — related to isoform expression, immune repertoire, expressed SNVs, and allelic imbalance — all in a single assay.

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Case study

Direct methylation detection with nanopore sequencing enables new view of multiple sclerosis

[The] benefits of concurrent analysis of sequence identity, base modifications, real-time, and cost-effective generation of genome-wide data support the application of [Oxford Nanopore Technologies] in studying the brain and spinal cord in different diseases.

Si et al. J. Neuroimmunol. (2023).

Si et al. utilised nanopore sequencing to directly detect methylation in brain samples from mice induced with experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS). Comparing to a control mouse group, they found 490 differentially methylated promoters; several of these genes had been flagged as relevant in previous MS studies, but methylation data had not been available. With this methylation data and additional metabolomic analyses, they were able to identify ‘a potential link between the dysregulation of promoter methylation and metabolome in the brain of EAE mice’.

Get started with multiomic nanopore sequencing

Find out how the application of multiomic nanopore sequencing is revolutionising human disease research.

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Nanopore multiomic sequencing toolkit

Nanopore multiomic sequencing applications Description Advantages Resources
Genomics & epigenomics Native DNA sequencing for variant detection, phasing, and best-in-class methylation detection — all from a single assay
  • Fast library prep — in as little as 10 min
  • Built-in methylation detection — simply turn on methylation detection during run set up
  • Save hands-on time and sample amounts with multiomic readout
  • Optimised, easy-to-use EPI2ME data analysis workflow
  • Perform targeted sequencing without additional library prep using adaptive sampling
    Whole-genome sequencing
    Transcriptomics & epitranscriptomics Native RNA sequencing for analysis of gene expression, splice variation, fusion transcript, and methylation — all from a single assay
    • Built-in methylation detection
    • Save hands-on time and sample amounts with multiomic readout
    • Optimised, easy-to-use EPI2ME data analysis workflow
    Gene expression
      RNA sequencing
      Single-cell & spatial transcriptomics Nanopore sequencing enables analysis of full-length cDNA — revealing previously hidden biology, including isoform diversity, alternative splicing, expressed variants, and transcripts for nonsense-mediated decay
      • Go from 10x Genomics cDNA to sequencing-ready library in ~3 hours
      • Optimised, easy-to-use EPI2ME data analysis workflow — no short-read sequencing required for cell barcode or UMI identification
      Single-cell sequencing
        10x Genomics application note
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        Which device for multiomic sequencing?

        Nanopore sequencing is uniquely scalable — from portable Flongle and MinION devices to the high-throughput benchtop GridION and PromethION devices, there’s a nanopore sequencing device to suit your multiomic analysis requirements.

        Recommended for multiomic sequencing

        PromethION 24

        Flexible, population-scale sequencing using up to 24 independent, high-capacity flow cells — complete genomic, transcriptomic, end epigenomic characterisation of large sample numbers.


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