Great comments so far on this issue! I've been asked this question a few times directly so thought I would share my thoughts with the community here, as I'm sure others have questions, too!!
For reference, I'm currently using the Genial line of kits that R-biopharm makes and am also running on a QuantStudio 5 thermocycler. Of all the options available when BDAS was initially investing in 2017-8, we got the best overall price and warranty from ThermoFisher for the QS5, which was less expensive than the Roche Lightcycler we also considered. While I had previously been using a smaller cycler with only 24 wells, it was already getting maxed out each run so we decided to invest in a larger unit for greater throughput. Plus, these two cyclers can both be used with many preexisting assays, or you can set them up with your own assays with SYBR Green and custom primers. Ultimately, I settled on the Genial kits from R-Biopharm.
The QS5 is on par with the Roche Lightcycler 480, Biorad CFX96, as well as the Gene Up cycler being distributed by Biomerieux in conjunction with the Invisible Sentinel real time kits (as opposed to their cartridge system). These are the "Cadillac" class of cyclers: all 96 well plate format (8 x 12 wells) with access to many of the commonly available fluorescent dyes. They also are 'open platforms' in that you could run with kits from Genial, Biotecon, Pika/Chia, or Invisible Sentinel, but are going to be the most expensive cycler option you could go for. A more mid-tier thermocycler you could consider is the My Go Pro, which has a 4 x 8 well heating block, still gives you an open platform similar to the above and is about a fifth of the cost of the average Cadillac class. Chia's unit (mentioned above) is slightly less robust as it only offers single or dual channel dye detection but this brings the overall price down to well below the Cadillacs as well. I have only demoed these kits and cycler, but the workflow is very similar across the board, and you can still get a lot of information with those 1-2 dyes.
SYBR Green assays are very inexpensive to run at $2-4 per sample, however it needs the most set up and input to get going because you have to source the items individually: from the primers to the enzymes and extraction buffers and all the other little bits you might need along the way. MBAA has some good resources from the past few years on which primers to use and some recommended DNA extraction kits to try if you decide to try and go this route instead of using a ready to use kit like one of the above. I attached a copy of Allagash Brewing Microbiologist Mike Billon's "Hacking PCR" as a good starting point for this method.
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Matt Linske
Manager and Lead Microbiologist
Brewing and Distilling Analytical Services
Denver, CO
720-450-7066
matt@bdastesting.com------------------------------
Original Message:
Sent: 03-20-2023 21:29
From: Volker Bornemann
Subject: Pall GeneDisk qPCR system suddenly being discontinued
I second Matt's approach. As a commercial testing laboratory, we refuse to invest into locked down one-trick-pony type of kits and devices. We use open, well established platforms, e.g., for PCR Thermo's Quant Studio, which was one of the first qPCR platforms approved for COVID. Other manufacturers, like Biorad, have open multi-channel platforms too, and there are numerous providers of kit and reagent manufacturers that give you competitive options. If you have an experienced micro- or molecular biologist on your team, they can even design, create, and validate their own assays. Or you can work with a contract research lab to do the same for you. Possibly a little higher initial cost/investment, but increased longevity and versatility, as you can easily adopt other tests that you might need in the future to your platform.
Good luck, and keep up the QC testing.
Best
Volker
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Volker Bornemann
President
Avazyme, Inc.
Research Triangle Park, NC
avazyme.com
Original Message:
Sent: 03-18-2023 08:36
From: Matthew Cottrell
Subject: Pall GeneDisk qPCR system suddenly being discontinued
This situation of discontinued, proprietary hardware and reagents is a strong argument for "open" PCR solutions such as the one offered by Chai.
I'm extremely satisfied with my dual channel Chai thermal cycler (https://www.chaibio.com/buy/openqpcr). I roll my own Lacto/Pedio and STA1 assays based on the primer sequences published in the Journal of the American Society of Brewing Chemists. I designed my own internal positive control using Lambda Phage DNA. And I use a Chelex based sample preparation method published in the Biotechniques journal.
For those needing a turn key solution the PCR reagents for detecting beer spoilage microbes produced by PIKA and available from Chai (https://www.chaibio.com/beer-spoilage) work great and are super user friendly.
And I've had great success as well using the PCR reagents from r-Biopharm (https://food.r-biopharm.com/industries/beer-analysis/) with the Chai instrument.
Plus, you'll be prepared for the next pandemic. The COVID-19 Surveillance kit (https://www.chaibio.com/covid-19) used to test our brewery staff on a weekly basis gave everybody in the building an added level of confidence that our company was taking extra measures to keep everybody safe while at work.
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Matthew Cottrell
Quality Manager and Microbiologist
Heavy Seas Beer
Baltimore MD
(302) 430-3489
Original Message:
Sent: 03-17-2023 11:42
From: Linus Hall
Subject: Pall GeneDisk qPCR system suddenly being discontinued
We got an email early this morning from Pall Corp that they were shutting down the plant in France that makes the GeneDisc PCR products and discontinuing the entire line. We tried to order from their online catalog and all of the GeneDisc kits had been removed.
It looks like we have an expensive machine that is going the way of the 8-track player. Anyone else in the same boat? What options are you looking at?
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Linus Hall
Owner
Yazoo Brewing
Madison TN
(615) 981-4649
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