Multiomics
[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, W. et al. J. Neuroimmunol. (2023)
Capture genomic, transcriptomic, and methylation data directly from native DNA/RNA in a single assay
Achieve full-genome coverage with unrestricted read lengths, including complex and repetitive regions
Explore isoforms, splicing, genotypes, and extensive variant detection with precise single-cell and spatial resolution
Reveal more biology in a single assay
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 enhance biomarker discovery.
Traditional multiomics approaches require multiple assays, platforms, and data analyses, resulting in complex and time-consuming workflows. Now, nanopore sequencing enables genomic, epigenomic, and transcriptomic — including single-cell, spatial, bulk, and targeted — analysis with any-length reads using streamlined workflows on a single platform. Nanopore technology generates ultra-rich data to shed light on complex biology, including single nucleotide variants (SNVs), structural variants (SVs), copy number variants (CNVs), short tandem repeats (STRs), haplotypes, DNA and RNA methylation, and full-length RNA transcript isoforms.
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Multiomic nanopore sequencing
Resolving the mechanisms underpinning human diseases is vital to understand disease phenotypes, identify novel biomarkers, and enable drug discovery. Find out how the application of multiomic nanopore sequencing is revolutionising human disease research.
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Taking multiomics to new lengths with Oxford Nanopore
Jonathan Mill (University of Exeter Medical School, UK) looks beyond DNA sequence variation to better understand complex diseases, with a focus on the central nervous system. Discover why he uses nanopore sequencing to uncover data missed with short-read sequencing.
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PromethION 24
Flexible, population-scale sequencing using up to 24 independently addressable, high-capacity flow cells — ideal for complete genomic, transcriptomic, and epigenomic characterisation of large sample numbers.
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Compact benchtop device designed to run and analyse up to five Flongle or MinION Flow Cells.
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Flexible, affordable, high-output nanopore devices for every lab — in a compact, accessible form.
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Flexible, large-scale, direct DNA and RNA sequencing devices — delivering on-demand access to terabases of data.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (20 bp to >4 Mb)
Short read length (<300 bp)
- Generate complete, high-quality genomes with fewer contigs and simplify de novo assembly
- Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
- Analyse long-range haplotypes, accurately phase single nucleotide variants (SNVs) and base modifications, and identify parent-of-origin effects
- Sequence short DNA fragments, such as amplicons and cell-free DNA (cfDNA)
- Sequence and quantify full-length transcripts to annotate genomes, fully characterise isoforms, and analyse gene expression — including at single-cell resolution
- Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
- Enhance taxonomic resolution using full-length reads of informative loci, such as the entire 16S gene
- Assembly contiguity is reduced and complex computational analyses are required to infer results
- Complex genomic regions such as SVs and repeat elements typically cannot be sequenced in single reads (e.g. transposons, gene duplications, and prophage sequences)
- Transcript analysis is limited to gene-level expression data
- Important genetic information is missed
Direct sequencing of native DNA/RNA
Amplification required
- Eliminate amplification- and GC-bias, along with read length limitations, and access genomic regions that are difficult to amplify
- Detect epigenetic modifications, such as methylation, as standard — no additional, time-consuming sample prep required
- Create cost-effective, amplification-free, targeted panels with adaptive sampling to detect SVs, repeats, SNVs, and methylation in a single assay
- Amplification is often required and can introduce bias
- Base modifications are removed, necessitating additional sample prep, sequencing runs, and expense
- Uniformity of coverage is reduced, resulting in assembly gaps
Real-time data streaming
Fixed run time with bulk data delivery
- Analyse data as it is generated for immediate access to actionable results
- Stop sequencing when sufficient data is obtained — wash and reuse flow cell
- Combine real-time data streaming with intuitive, real-time EPI2ME data analysis workflows for deeper insights
- Time to result is increased
- Workflow errors cannot be identified until it is too late
- Additional complexities of handling large volumes of bulk data
Accessible and affordable sequencing
Constrained to centralised labs
- Sequence on demand with flexible end-to-end workflows that suit your throughput needs
- Sequence at sample source, even in the most extreme or remote environments, with the portable MinION device — minimise potential sample degradation caused by storage and shipping
- Scale up with modular GridION and PromethION devices — suitable for high-output, high-throughput sequencing to generate ultra-rich data
- Perform cost-effective targeted analyses with single-use Flongle Flow Cells
- Sequence as and when needed using low-cost, independently addressable flow cells — no sample batching needed
- Use sample barcodes to multiplex samples on a single flow cell
- Bulky, expensive devices that require substantial site infrastructure — use is restricted to well-resourced, centralised locations, limiting global accessibility
- High sample batching is required for optimal efficiency, delaying time to results
Streamlined, automatable workflows
Laborious workflows
- Prepare samples in as little as 10 minutes, including multiplexing
- Use end-to-end whole-genome, metagenomic, targeted (including 16S barcoding), direct RNA and cDNA sequencing workflows
- Scale and automate your workflows to suit your sequencing needs
- Perform real-time enrichment of single targets or panels without additional wet-lab prep by using adaptive sampling
- Lengthy sample prep is required
- Long sequencing run times
- Workflow efficiency is reduced, and time to result is increased
