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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

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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) Read length

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 DNA

  • 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 Run time

  • 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 Time icon

  • 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.

White paper

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.

Case study

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.

Case study

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

Case study

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. 
 

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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.

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Nanopore sequencing yield chart

Recommended for human genome assembly

PromethION 2 and PromethION 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.

PromethION 48

With 48 independently addressable, high-yield flow cells and powerful, integrated compute, PromethION 48 delivers highly accurate genome assemblies at population scale.

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PromethION P24

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

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GridION

From genome assembly to gene expression, run multiple experiments on-demand using 5 independent MinION flow cells.

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MinION

Access the benefits of nanopore technology from just $1,000 — suitable for targeted sequencing and gene expression studies.

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MinION Mk1C

Integrated sequencing and analysis in a powerful handheld device — suitable for targeted sequencing and gene expression studies.

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Flongle

Adapting MinION and GridION for smaller, routine tests and analyses. Low plex targeted sequencing, RNA isoform analysis, and quality control applications.

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VolTRAX

Automated sample extraction and library preparation.

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