Multiomics
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.
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.
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
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.
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’.
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 |
| Epigenetics |
| Transcriptomics & epitranscriptomics | Native RNA sequencing for analysis of gene expression, splice variation, fusion transcript, and methylation — all from a single assay |
| Gene expression |
| 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 |
| Single-cell sequencing |
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.
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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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With 48 independently, high-yield flow cells and powerful, integrated compute, PromethION 48 is our highest-throughput device — delivering complete genomic, transcriptomic, and epigenomic characterisation of large sample numbers.
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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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With two independent, high-output PromethION Flow Cells, compact PromethION 2 devices bring the benefits of high-coverage, real-time nanopore sequencing to every lab.
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From genome assembly to gene expression, run multiple experiments on-demand using five independent MinION or Flongle Flow Cells.
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Access the benefits of nanopore technology from just $1,999. Suitable for multiomic analysis of small genomes, transcriptomes, and epigenomes.
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Adapting MinION and GridION for smaller, routine tests and analyses. Suitable for analysis of microbial cultures, low plex targeted sequencing, RNA isoform analysis, and quality control applications.
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