Acoustic deparaffinization instruments

FFPE as a sample type has always been a valuable resource for diagnosis and confirmation, but it’s sample prep for NAP and subsequent analysis is gated behind lengthy procedures for removing the paraffin cask. Typically this is achieved either by lengthy mineral oil bath or Xylene (flammable, organic solvent, nasty stuff), neither of which can automated without concerns. I work for a company operating solely in the NAP space, and ran into quite a few folks at AMP conference recently who were frustrated by the lack of automation during this deparaffinization step. Most scientists wanted the hands-free convenience of automation, but didn’t expect the solution to be 4-12 hours in hot mineral oil that would be ridiculous to slap into their existing liquid handlers.

One method that’s been interesting is acoustic devices from companies like Covaris or Diagenode that can reduce the procedure down to 15 minutes, albeit requiring consolations in the protocol such as special buffers and glass labware. The instruments are expensive; and as such there’s not much I can find from my supporting cast on how well these instruments integrate into your Hamiltons or Tecans in the labspace. Does anyone have any experience with these instruments or how a workflow looks and if full integration is possible? I imagine that the biggest hurdle would be your reagent space, and having to work with glass labware, but I’m interested in hearing what y’all think.

I’d suggest contacting Covaris, they should be able to answer your questions in detail. I believe they have a pretty slick youtube video of the process on a Lynx, and I think they are automation agnostic and the process could be automated on a Hamilton.

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This is awesome! Exactly what I was looking for; I just didn’t know where to look. Have you ever worked with that instrument, automated or not?

I haven’t worked with the Lynx. I primarily work on Hamiltons. I don’t know anyone that has this process on the Hamilton, but it shouldn’t be too difficult to implement provided that you have the automation resources/team.

In regards to the setup, I believe all the consumable items needed for the process is sold as a kit, and I think you’ll need to get their on deck ultrasonicator.

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At Hamilton, we’re actively working on a solution with Covaris. Should have an update in Q1 of 2023. In the meantime, please coordinate with your local sales rep if interested!


I’ve worked with the Lynx extensively and I like them but if you’re doing anything complex, you may want to work with a more established player who has tested production supply chain lines…