Resources Get started
Home > Applications > Targeted sequencing

Targeted sequencing with nanopore technology

The long sequencing reads delivered by nanopore technology expand 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 analysis provides immediate access to results and enables sequencing to be stopped once sufficient coverage or a result is obtained. All common targeting and enrichment strategies can be utilised, including PCR amplification (amplicon), hybridisation-based capture, and CRISPR/Cas-mediated 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
  • Rapid workflows, including 16S rRNA, and real-time results
  • Detect base modifications using direct targeted sequencing approaches

How will you use targeted nanopore sequencing?

Human and clinical research

Microbiology and infectious disease

Plant and animal research

Long, targeted, nanopore sequencing reads enable 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 the 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, CRISPR/Cas9
  • Detect base modifications using direct sequencing
  • Analyse data in real time — immediate access to results

‘The Oxford Nanopore MinION can detect missense mutations and an exonic deletion in this difficult gene [GBA], with the added advantage of phasing and intronic analysis’

Leija-Salazar et al

William Jeck: Nanopore sequencing and rapid fusion testing – a ‘killer app’ in molecular pathology

Targeted sequencing is commonly employed to aid the rapid identification and characterisation (e.g. antimicrobial resistance) of microorganisms. Long-read nanopore sequencing 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
  • 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, CRISPR/Cas9
  • Explore epigenetic modifications using amplification-free enrichment
  • Analyse data in real-time — stop when result obtained, wash flow cell and reuse

Targeted sequencing provides a cost-efficient method of analysing specific genomic regions of interest. Long-read, real-time nanopore sequencing expands upon the traditional SNV analysis provided by short-read technologies to also enable the characterisation of structural variants, repetitive regions, and phasing. In addition, amplification-free target enrichment techniques 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

Crystal Gigante: Evaluation of the Oxford Nanopore MinION for Rabies Virus Sequence Typing

Open a chat to talk to our sales team