Inside a Cepheid GeneXpert Cartridge

I previously wrote about Cepheid, and what it might take to create a Cepheid/GeneXpert like DNA sequencing instrument. It’s been speculated that Cepheid cartridges cost $3 to make.

I figured it would be fun to buy some and pull them apart and see exactly what’s in a GeneXpert kit, so I grabbed some cartridge off eBay. The full kit contains the cartridge, guidance, poster format protocol and a CD. The CD has documentation in pdf format and a series of ADFs (Assay Definition Files). The ADFs are ASCII encoded hex data, the first few bytes are FCC2279597DBE28F2689F83C183692B76B. I tried converting the hex to binary, but nothing sensible popped out. The file contain repeated segments, suggesting they are not encrypted. But the file likely contains all recipe information needed to run the test and perform the necessary analysis and reporting.

They are regular writable CDs, and this is kind of an interesting decision in a world where we mostly receive software updates online. Most likely many GeneXpert instruments are installed in locations where there is no Internet access, or where they need to be kept isolated from the big bad Internet.

Looking at the external parts of the cartridge, you can see a qPCR reaction chamber which is very similar to that use of Cepheid’s previous generation of instruments (the SmartCycler). In the image below, a SmartCycler reaction tube is shown on the left for comparison:

The reaction tube is designed to have thin walls to enable fast thermal cycling. In both cases this is a separate piece of plastic film bonded to the cartridge body.

Surprisingly, Cepheid seem to do injection molding in-house. The film looks like it’s thermally bonded. I suspect they’d need a QC step where they pressure test the integrity of this.

Opening the cap breaks seals over 13 apertures on the top on the cartridge, these allow air to be drawn into the cartridge to allow fluid to flow between chambers:

To investigate the cartridge any further, we need to start hacking it apart. But we can get some information from the documentation:

So, we’re expect to find ~6 mL of reagents and some beads. And indeed we do find 3 filled reagent compartments:

These are the lysis, binding and elution reagents. Digging further we can also find the beads mentioned, but only in two chambers:

Looking at the chambers side on, we can see that they are not completely filled with a single bead type. Further down, there’s a barrier (which is a waxy material) and a blue bead:

So, making guesses about what’s happening here, the input material is initially combined with the lysis mix. Somewhere in this cartridge I imagine there must be a silica beads/substrate, while there are alternative RNA/DNA-binding materials Cepheid patents mention this explicitly and it seems like the most likely option. So one of these sets of beads is likely Silica.

The elution reagent then releases the bound material. The other beads must contain the reverse transcriptase and PCR master-mix. These are lyophilized (freeze dried) and reconstuted during the run.

The cartridge contains a self-contained plunger based fluidic system which pushes the reagents around, there’s neat description of the approach in this patent and YouTube videos.

Pulling apart the valve, you can see how this is constructed:

The instrument can rotate the valve to one of 13 positions which selecting different fluidic connections. There’s what seems to be a silicone gasket bonded to the cartridge body. The instrument pushes a rod into the black rubber gasket in the center of the valve. This is barrier between the internal fluid and instrument. By pulling it up and down the instrument can push and pull reagents around without making a direct fluidic connection to the cartridge.

Conclusion

The cartridge is clearly well engineered and actually more complex than I expected. However most of the complexity is in injection molded parts. These appear to have been engineered to relatively tight tolerances, and there are lots of different materials here. I suspect this is part of the reason why they do the injection molding in-house.

But injection molding is cheap, $3 might be an under-estimate here, but even if these cartridges cost $5, it’s impressive how much you can get done with such a small budget.