Human genomics
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'One of the real powers of this technology is not just being able to detect DNA methylation, but also to directly read out DNA hydroxymethylation'
Jonathan Mill, University of Exeter Medical School, UK
Generate unprecedented insights for human genomics research
With real-time, multiomic nanopore sequencing, you can discover previously hidden human genomic, epigenomic, and transcriptomic variation — from the population level down to the single-cell level.
Fully characterise challenging regions that cannot be resolved with legacy short-read sequencing technologies. Detect single nucleotide variants (SNVs) and short tandem repeats (STRs), generate highly contiguous genomes by spanning repeat regions and structural variants (SVs), interrogate full-length RNA transcript isoforms, and identify DNA and RNA base modifications, such as methylation, as standard.
With nanopore technology, there is no limit to read length (current record >4 Mb), allowing you to reveal critical insights for human genomics research — from developmental biology and rare disease genomics to common complex diseases.
Featured content
Advancing human genomics with nanopore sequencing
Learn how researchers are utilising nanopore sequencing to characterise all forms of human genomic variation, from repeat regions, SVs, and phasing to full-length transcript isoforms and methylation — delivering a comprehensive understanding of the human genome and genetic disease.
Comprehensive human genomic variant and methylation analysis
From sample to answer, discover how nanopore sequencing delivers comprehensive human variation detection in this best practice, end-to-end workflow. Get accurate SNV, SV, STR, and methylation results in a single streamlined assay, with integrated tertiary analysis.
Pharmacogenomics with Oxford Nanopore sequencing
Pharmacogenomics (PGx), the study of genomic-driven response to treatments, includes some of the genome's most challenging genes. Conventional array and legacy sequencing technologies are incapable of fully resolving the problems presented by pseudogene homology, haplotyping requirements, and complex structural variants.
Oxford Nanopore sequencing delivers the capabilities to fully resolve all the PGx variants with a single technology and a single assay. You can choose from two different methods to achieve full resolution PGx: (1) hybrid capture; and (2) adaptive sampling.
Recommended device for human genome sequencing
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PromethION 24
The PromethION 24 device combines 24 independently addressable, high-capacity flow cells with powerful, integrated compute. The device delivers flexible, on-demand access to terabases of sequencing data — ideal for cost-effective, high-throughput sequencing of human genomes and transcriptomes.
Featured analysis for human genome sequencing
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EPI2ME wf-human-variation
The EPI2ME wf-human-variation workflow provides all-in-one calling and phasing of SNVs, SVs, copy number variants (CNVs), short tandem repeats (STR) expansions, and methylation — covering both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (50 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
- 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
