Human genomics
Fully characterise human genetic variation with real-time nanopore sequencing technology. Generate highly contiguous genomes or interrogate targeted regions and full-length RNA transcripts. With nanopore technology, there is no limit to read length (current record >4 Mb), enabling complete resolution of challenging regions, uncovering previously hidden variation. Plus, identify base modifications as standard, with amplification-free native DNA or RNA sequencing.
The potential of ultrarapid nanopore genome sequencing for critical care medicine
we present a pipeline for high-depth nanopore sequencing of a human genome in less than 2 hours...
Goenka, S.D et al. Nat. Biotechnol. 40(7), 1035–1041 (2022)
Oxford Nanopore sequencing
Traditional short-read technologies
Unrestricted read length (>4 Mb achieved)
- Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
- Assemble high-quality genomes, with fewer gaps
- Analyse long-range haplotypes and phasing
- Fully characterise transcript isoforms, splice variants, and fusions — up to single-cell resolution
Read length typically 50–300 bp
Short reads do not typically span entire regions of interest, including repeats and structural variants, or full-length RNA transcripts, resulting in fragmented assemblies and ambiguous transcript isoform data.
Direct, amplification-free protocols
- Detect base modifications, such as methylation, as standard — no additional prep required
- Eliminate amplification bias and read length limitations
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.
Real-time data streaming
- Stop sequencing when sufficient data generated — wash and reuse flow cell
- Immediate access to results
- Perform target enrichment without additional wet-lab prep using adaptive sampling
Fixed run time with bulk data delivery
Increased time-to-result and inability to identify workflow errors until it’s too late, plus additional complexities of handling large volumes of bulk data.
Flexible and on demand
- Sequence what you need when you need it — no sample batching required
- Scalable devices to suit your needs — from low throughput to thousands of human genomes per year
- Get flexible throughput with modular GridION and population scale with PromethION devices
- No sample batching required
Limited flexibility
Sample batching may be required for optimal efficiency, potentially delaying results.
Advancing human genetics research with nanopore sequencing
From closing genome gaps to characterising full-length RNA transcripts, this White paper describes how real-time, on-demand nanopore sequencing technology is being used to address the limitations of traditional short-read sequencing technologies to deliver novel biological insights. Specific case studies reveal how researchers are applying the benefits of nanopore technology to a variety of sequencing techniques, including whole genome, targeted, and RNA sequencing.
View more content on getting started with nanopore sequencing for human genomics, including guides and workflows on genome assembly, variant calling and phasing, and methylation detection.
Accessing the inaccessible human genome with long reads
The human genome contains 36,794 ‘dark’ regions that are intractable to assembly and alignment using traditional short-read sequencing technology. Discover how, Ebbert et al. applied long nanopore sequencing reads to resolve these regions.
Oxford Nanopore Technologies outperformed other long-read technologies, resolving 90.4% of dark CDS [coding sequence] regions
From genome assembly to single-cell sequencing, whatever your research interests, get comprehensive information in our Investigations pages.
Expanding studies of global genomic diversity with complete assembly of diploid human genomes
Nanopore sequencing is enabling the creation of multiple reference genomes that better represent human genomic diversity. Until recently, assemblies had been focused exclusively on a single haploid cell line of European ancestry and did not reflect the diversity of the genome or represent a diploid genome. Now, scientists are utilising nanopore sequencing to create more human reference genomes reflecting the diversity of human genomes. In 2022, the Telomere-to-Telomere (T2T) consortium finished the first complete sequence of a human genome, representing gapless assemblies for all 22 autosomes plus chromosomes X and Y, including around 200 Mb of previously unresolved sequence.
At the NCM2022, Karen Miga (University of California, Santa Cruz) presented the work of the Human Pangenome Reference Consortium, a multi-centre programme aiming to improve representation of global genome diversity by sequencing over 350 diploid genomes from diverse sources. To achieve this, ultra-long nanopore reads from whole genomes, sequenced to a depth of 30x, will be obtained for each human diploid genome, and assembled using the tool Verkko. The availability of these complete, telomere-to-telomere assemblies will revolutionise human genetics and genomics, providing a truly representative global genomics resource.
We can study the genome end to end ... this is what it means to be comprehensive
Karen Miga, University of California, Santa Cruz
Nanopore long-read sequencing for full-genome assemblies of Indigenous communities
In partnership with the National Centre for Indigenous Genomics, Dr Andre Reis and his team at the Garvan Institute of Medical Research, Australia are using population-scale, whole-genome nanopore sequencing to build a detailed catalogue of repetitive, structural, and complex genetic variation across Australian Indigenous communities. Indigenous Australians have a rich and unique genetic diversity that is currently missing from global genomics resources. This limits the ability to understand genetic disease in Indigenous families. Failure to address this representation gap will lead to increasing inequity in the benefits of genomic medicine, exacerbating health disparities between Australia's Indigenous and non-indigenous communities.
At the NCM 2022, Andre reported that his team have performed whole-genome nanopore sequencing of 68 genomic samples from individuals from four Indigenous communities in Northern Australia. They are using the data to explore the unique genetic variation among Indigenous Australians at unprecedented resolution. Andre highlighted how this work will lead to the creation of genomics resources enabling research that will be critical to achieving equitable outcomes in genomic medicine in Australia.
Scalable sequencing for human genomics
From portable, yet powerful Flongle and MinION devices to the high-throughput benchtop GridION and PromethION platforms — scale your sequencing to match your specific research requirements.
* Theoretical max output (TMO). Assumes system is run for 72 hours (or 16 hours for Flongle) at 420 bases / second. Actual output varies according to library type, run conditions, etc. TMO noted may not be available for all applications or all chemistries.
† PromethION P2 and P2 Solo devices are currently preorder, with Early Access devices expected to ship in 2022.
PromethION 2 & 2 Solo
Offering the flexibility of two independent, high-output PromethION Flow Cells, the compact PromethION 2 devices bring the benefits of high-coverage, real-time nanopore sequencing to every lab. Ideal for low-cost access to highly accurate human genomes and transcriptomes.
With 48 independently addressable, high-yield flow cells and powerful, integrated compute, PromethION 48 delivers highly accurate genome assemblies at population scale.
Flexible, population-scale sequencing using up to 24 independent, high-capacity flow cells — complete genomic and transcriptomic characterisation of large sample numbers.
From genome assembly to gene expression, run multiple experiments on-demand using up to five independent MinION Flow Cells.
Access the benefits of nanopore technology from just $1,000 — suitable for targeted sequencing and gene expression studies.
Integrated sequencing and analysis in a powerful handheld device — suitable for targeted sequencing and gene expression studies.
Adapting MinION and GridION for smaller, routine tests and analyses; ideal for low-plex targeted sequencing, RNA isoform analysis, and quality control applications.
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