ONT + Cepheid
There’s not that much information about the Cepheid-Nanopore deal. Keith did a great write up previously. But given that it was mentioned again in Oxford’s H1 call, I thought it would be interesting to do a little more digging.
There’s this video with about 400 views which contains the following statement:
“it’s just a different cartridge that’s being used for next-generation sequencing instead of PCR diagnostics” 1
Similarly Oxford’s press release states: “Cepheid’s GeneXpert system for pre-sequencing sample and library preparation”.
To me this seems pretty clear, Cepheid are developing a new cartridge for the GeneXpert which can process raw samples into a library.
That seems like a modest goal, but it’s also awesome!
This is pretty much where we ended up with the ubiquitous metagenomic sequencing. A simple fixed workflow cartridge that automates the sample and library prep for infectious disease testing. In our case, with a few to metagenomic sequencing for pandemic preparedness.
Having pulled apart a cartridge (and instrument), the Cepheid cartridge seems well suited to library prep. In fact the Cepheid approach may be overkill for this application2.
The mechanical side of the product should be relatively simple, changes will be required to allow material to be removed from the cartridge3 but that’s about it.
The difficulty will come around reliably producing libraries from somewhat heterogeneous samples. I assume multiplexing will be impractical, so a single cartridge will be paired with a single MinION flowcell. That should simplify things, but also makes this quite an expensive product compared to the (<$20) regular Cepheid cartridge.
All together we’re likely looking at a ~$700 per sample test.