Nanopore sequencing is established as a powerful tool for the analysis of genomic variants.
How can nanopore sequencing support your cancer research?
- Targeted re-sequencing for in-depth analysis of inherited or somatic variations, using hybridisation capture or amplicons for the analysis of
- cancer associated genomic loci
- specific gene panels
- RNA sequencing for analysis of splice variants and fusion transcripts
- Whole genome sequencing using long read technology aids the comparison of tumour and normal genomes:
- understanding of structural variants
- discovery of previously unidentified SNVs
Sequencing accelerates the analysis of cancer associated alterations in genome sequence such as insertions and deletions, CNVs, inversions, duplications, translocations and gene fusions, as well as single nucleotide variants.
Nanopore sequencing gives you:
Ultra-long reads spanning difficult and repetitive regions
Nanopore sequencing processes the fragment length presented to it, enabling ultra-long reads. The longest recorded so far is >500Kb. This allows researchers to investigate structural variations whether looking at repeats, inversions, indels, or translocations, as well as SNVs. When investigating fusion transcripts and their role in cancer, long reads are optimal for analysing the full length transcripts and understanding the re-arrangements that have taken place.
The same technology and methods are used on
- MinION, the portable sequencer that now delivers 10Gb of 1D data per Flow Cell in 48 hours
- PromethION, with a modular design but designed for 280x the sequencing capacity of MinION
allowing you to work on either, depending on the scale of your experiment.Nanopore sequencing in cancer research
Speed, small footprint and low capital cost for on-demand sequencing
Nanopore sequencing data starts streaming immediately, rather than being delivered at the end of a 'run'. Real-time data streaming allows immediate analysis and you can decide, if the experiment is progressing as expected, when sufficient data has been generated for the experiment and when to move onto the next one.
At only $1,000 for a starter pack and fully portable, the MinION allows you to explore nanopore sequencing in your cancer research. Combining long PCR amplificaton and long reads it is possible to reduce the number of PCR reactions required per sample, removing the need for a PCR for each exon. Dependent on the target size and the depth of coverage required it is possible to use barcoding, giving the opportunity to further optimise the cost per sample.Structural variant analysis
Batch or sequential sample analysis, you choose
When using a targeted sequencing approach you may be choosing between sequence capture or amplicons. For either, you can combine samples using barcoding. By using you can examine the same target region across multiple samples in one experiment; for sequence capture this is possible with up to 12 samples, while with amplicons up to 96 barcodes are possible.
Only nanopore sequencing allows you to do on-demand sequencing at no extra cost. Your experiment can be run:
- with just one sample
- with multiple samples loaded sequentially or
- simultaneously with barcoded batches of sample
How are others using nanopore sequencing in cancer research?
View these publications and movies to find out more.