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Cancer research with nanopore sequencing technology

Fully characterise tumour samples using long-read, real-time nanopore DNA and RNA sequencing. Long nanopore reads deliver comprehensive analysis of somatic mutations, structural variation – including insertions, deletions, and translocations – phasing, fusion transcripts, and base modifications.

  • Resolve structural variation, breakpoints, and phasing using long reads
  • Study isoforms, splice variants, and fusion transcripts from full-length RNA reads
  • Rapid 10-minute library prep and low DNA input requirements
  • Eliminate bias and identify epigenetic modifications with direct sequencing
  • Get faster access to results with real-time analysis
  • Scale to your needs using Flongle, MinION, GridION, or PromethION

How will you use nanopore technology?

Accurately identify structural variants

Characterise the complete cancer genome

Sequence targeted regions

Analyse the cancer transcriptome

Identify epigenetic modifications

Long sequencing reads enable resolution of challenging genomic rearrangements commonly found in cancer samples, including deletions, insertions, duplications, inversions and translocations. Using nanopore sequencing, read lengths in excess of 2 Mb have been generated.

Based on current internal flow cell performance of 200 Gb (October 2018).
  • Accurately resolve structural variants using long sequencing reads
  • Use whole genome or targeted approaches
  • Precisely detect breakpoint junctions
  • Streamline your workflow with 10-minute library prep and real-time data analysis
  • Get high yields, on demand — 1.8 Gb Flongle; 30 Gb MinION; 150 Gb GridION;
    4,800/9,600 Gb PromethION

‘The comprehensive characterization of SVs using the robust long-read sequencing approach in cancer cohorts will facilitate strategies to monitor genome stability during tumor evolution and improve therapeutic intervention’

Gong et al

Wigard Kloosterman: Nanopore sequencing of cancer genomes

Whole genome sequencing using direct, long-read nanopore sequencing technology delivers unprecedented insight into the cancer genome. Fully characterise the cancer genome and discover novel cancer biomarkers.

  • Accurately resolve structural variation and breakpoints
  • Phase distal somatic mutations
  • Simplify genome assembly using long and ultra-long reads
  • Detect epigenetic modifications alongside nucleotide sequence
  • Get high yields, on demand — 1.8 Gb Flongle; 30 Gb MinION; 150 Gb GridION;
    4,800/9,600 Gb PromethION

‘Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost’

Euskirchen et al

Wigard Kloosterman: Nanopore sequencing of cancer genomes

Targeted sequencing using long nanopore sequencing reads allows you to focus on specific genes or regions with known cancer associations. Characterise exons, introns, promoters, repetitive regions and structural variation in a single read — with no assembly required.

  • Cost-effectively characterise large genomic regions of interest – use Flongle for up to 1.8 Gb real-time data for $90 per flow cell
  • Uncover 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
  • Detect epigenetic modifications using direct sequencing
  • Don’t wait for results – analyse data in real time
     

‘Given the speed, small footprint, and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of cancer-associated SVs needed for molecular relapse, early detection, or therapeutic monitoring’

Norris et al

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

Utilise long reads to sequence full-length cDNA or direct RNA transcripts to reveal the true cancer transcriptome — even from single cells. Determine isoform expression, identify chimeric transcripts and study tumour progression. Use long reads to distinguish clonal and polyclonal variants.  

  • 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 RNA
  • A simple, cost-effective, and scalable solution for any lab
  • New: Get higher yields from less input using the latest RNA and cDNA sequencing kits

Epigenetics is an increasingly important area of cancer research and base modifications have significant potential as diagnostic and prognostic indicators of disease. Direct nanopore sequencing does not require amplification, strand synthesis or bisulfite conversion, allowing detection of modified DNA or RNA bases alongside the nucleotide sequence.

  • Cost-effectively identify modified bases with 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 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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