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Targeted sequencing with nanopore technology

Enabling the generation of any length of sequencing read — from short to ultra long — nanopore technology expands the capabilities of targeted sequencing approaches beyond the analysis of single nucleotide variants (SNVs), to include cost-effective, high-coverage characterisation and phasing of structural variants (SV), repetitive regions, and base modifications. Real-time data streaming provides immediate access to results and enables sequencing to be stopped once sufficient coverage or a result is obtained. Real-time analysis also underpins Oxford Nanopore's unique enrichment method of adaptive sampling, where reads can be selected or rejected for further sequencing based on their sequence composition — removing the traditional, time-consuming requirement for upstream wet lab-based enrichment.

  • Discover more — sequence entire genes or genomic regions in a single read
  • Characterise structural variation, repetitive regions, single nucleotide variants, and phasing
  • Your choice of enrichment strategy — amplicon, hybrid-capture, CRISPR/Cas9, or adaptive sampling
  • Rapid workflows, including 16S rRNA, and real-time results
  • Detect base modifications using direct targeted sequencing approaches, such as adaptive sampling

How will you use targeted nanopore sequencing?

Human and clinical research

Plant and animal research

Microbiology and infectious disease

The facility to generate any length sequencing reads, including ultra-long reads (>4 Mb), enables entire genes and genomic regions of interest to be fully characterised, allowing researchers to look beyond a handful of known variants. This can include novel variants in gene promoters, introns, and repetitive regions, plus simultaneous analysis of structural variants, base modifications, and phasing. 

  • Characterise large genomic regions and entire genes in single reads
  • Resolve structural variants, repetitive regions, SNVs and phasing
  • Choose your enrichment strategy — PCR, hybrid-capture, adaptive sampling, or CRISPR/Cas9
  • Detect base modifications using direct amplification-free sequencing of native DNA
  • Analyse data in real time — immediate access to results

Targeted sequencing provides a cost-efficient method of analysing specific genomic regions of interest. Long nanopore sequencing reads generated in real-time enables the characterisation of structural variants, repetitive regions, and phasing and therefore allows for a more expansive analysis compared to what can be achieved using short-read data. In addition, amplification-free target enrichment techniques, such as adaptive sampling, combined with direct nanopore sequencing allows the identification epigenetic modifications alongside the nucleotide sequence — further expanding the utility of targeted sequencing. 

  • Cost-effectively screen large and targeted regions of interest for known and novel variants
  • Identify haplotype-specific markers by phasing long reads 
  • Resolve structural variants, repetitive regions, and SNVs
  • Characterise transgene insertions and gene editing events
  • Identify plant and animal pathogens in real time
  • Explore epigenetic modifications using amplification-free enrichment

‘With its rapid library preparation protocol, real-time sequencing mode and the capability to sequence large DNA fragments with currently increasing accuracy the MinION is an attractive tool to quickly characterise samples of interest’

Giolai et al

Lara Urban: Leveraging adaptive sampling of environmental DNA for monitoring the critically endangered kākāpō

Targeted sequencing is commonly employed to aid the rapid identification and characterisation (e.g. antimicrobial resistance) of microorganisms. Long nanopore reads enables larger regions of interest to be characterised, enhancing the analysis of repetitive regions and improving taxonomic assignment. Multiplexing offers cost-effective analysis of multiple samples, while real-time data streaming delivers immediate access to results. 

  • Characterise large regions of interest in single reads and enhance taxonomic resolution
  • Resolve structural variants, repetitive regions, and SNVs
  • Sequence in the lab or at sample source using the portable MinION
  • Choose your enrichment strategy — PCR, hybrid-capture, adaptive sampling, or CRISPR/Cas9
  • Explore epigenetic modifications using amplification-free enrichment
  • Analyse data in real-time — stop when result obtained, wash flow cell and reuse

‘We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15–60 min’

Quick et al

Adriel Latorre-Pérez: A round trip to the desert — in situ nanopore sequencing informs targeted bioprospecting