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Home > Applications > Population-scale genomics

Population-scale genomics with nanopore sequencing technology

Delivering terabases of data, the recently-launched PromethION brings the benefits of long-read nanopore sequencing to large-scale population studies. PromethION is designed to run up to 24 (P24) or 48 (P48) flow cells at any time, with each one capable of producing more than 200 Gb of data. Capital-free packages, and flow cell pricing reaching as little as $625 per flow cell, allows researchers to cost-effectively sequence, assemble, analyse and compare whole genomes, targeted regions, methylation profiles and transcriptomes from 10’s to 1,000’s of samples.

Streamlined, automatable protocols with low input requirements are available. Generate optimised workflows with our online Protocol Builder — available to all Nanopore Community members.

Use as little as 1 ng (PCR-based) or 400 ng (PCR-free) input DNA. Workflows compatible with automated preparation platforms – scripts available (contact us).
  • Identify, resolve and compare structural variation, repetitive regions, SNVs and phasing for 1000's of samples
  • Simplify de novo assembly — build and correct population- and species-specific reference genomes
  • Fully characterise, quantify and compare transcript isoforms across large populations
  • Eliminate bias and identify epigenetic modifications with direct DNA or RNA sequencing
  • Streamlined, automatable workflows with low input requirements
  • Scale to your population needs using GridION or PromethION

What is your large-scale project?

Population-scale genome sequencing

Analysis of targeted regions

Population transcriptomics

Epigenetics research

PromethION is now being used in population-scale sequencing projects around the world.  High-throughput, long reads enable the resolution of challenging genomic regions and the delivery of more complete and contiguous genome assemblies – providing the foundation for accurate population genetics studies. Fragment length equals read length, allowing users to choose long or ultra-long reads to suit their requirements. 

Based on current internal flow cell performance of 200 Gb (October 2018), assuming 48 flow cells.
  • Simplify de novo assembly — create new reference genomes or correct and complete existing genomes
  • Rapidly identify, resolve and map novel and common structural variants within large populations
  • Define, map and compare repetitive regions
  • Investigate linkage and define haplotype phasing
  • Detect epigenetic modifications alongside nucleotide sequence
  • High yields, on demand —capacity of  4,800/9,600 Gb PromethION P24/P48 or 150 Gb if using GridION

‘Oxford Nanopore’s long-read sequencing capability creates a window into parts of the genome that have been out of reach, as well as giving us a much better handle on structural variants that confer risk of a wide variety of diseases. We have used Oxford Nanopore technology to sequence several hundred human genomes and continue to see the promise of this emerging technology’ 

Kári Stefánsson, CEO, deCODE Genetics

PromethION High-throughput sequencing device

Where sample numbers are large and specific genes or pathways have been identified, it may be advantageous and to target and sequence specific genomic regions using long nanopore reads. Characterise specific genes, exons, introns, promoters, repetitive regions and structural variation in their entirety in single, full-length reads — with no assembly required. Multiplex samples for cost-effective population genetics studies. 

  • Cost-effectively characterise large genomic regions of interest within large populations
  • Uncover previously hidden variation – sequence entire genes, including exons, introns and promoters in single reads
  • Resolve structural variants, repetitive regions and phasing using long-reads
  • Your choice of enrichment strategy – PCR, hybrid-capture, CRISPR/Cas9
  • New: Fully integrated Cas9 Sequencing Kit — cost-effective, amplification-free enrichment
  • Detect epigenetic modifications using direct sequencing
  • Don’t wait for results – on demand sequencing and analysis of data in real-time
  • High yields, on demand —capacity of  4,800/9,600 Gb PromethION P24/P48 or 150 Gb if using GridION

‘The rapid evolution of specific bioinformatic methods, and the improvements in accuracy and data yield, combined with the minimal footprint and capital investment, make the MinION a suitable platform for long-read sequencing of difficult genes such as GBA’

Leija-Salazar et al

Detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

Full-length, long reads allow reliable characterisation, quantification and comparison of the full complexity of gene expression profiles between cohorts.

  • Full-length transcripts — unambiguous identification of splice variants and gene fusions
  • Accurate transcript and isoform quantification
  • Eliminate PCR bias using direct cDNA or direct RNA sequencing
  • Detect base modifications alongside nucleotide sequence using direct sequencing
  • Easy identification of anti-sense transcripts and lncRNA isoforms
  • New: Get higher yields from less input using the latest RNA and cDNA sequencing kits

Direct nanopore sequencing does not require amplification, strand synthesis or bisulfite conversion, reducing bias and allowing detection of modified DNA or RNA bases alongside the nucleotide sequence. The facility to simultaneously identify and phase nucleotide sequence alongside base modifications, combined with the high-throughput offered by the PromethION platform opens new avenues of investigation in population genetics. 

  • Cost-effectively identify modified bases and nucleotide sequence
  • Capture base modifications as standard – analyse when you are ready
  • Rapid 10-minute library prep – no bisulfite conversion required
  • Phase modified bases using long reads
  • Analyse data using Tombo, one of a growing number of tools

‘Methylation data can directly be obtained from the same WGS data set which makes time-consuming bisulfite conversion and specialized methylation assays (sequencing or hybridization-based) expendable’

Euskirchen et al

Cas9 targeted enrichment for nanopore profiling of methylation at known cancer drivers

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