3 ms·

This is the device - http://www.cepheid.com/en_US/systems/GeneXpert-Family-of-Systems/GeneXpert-Xpress http://www.cepheid.com/en_US/systems/GeneXpert-Family-of-

by js2 7y ago

This is the device - http://www.cepheid.com/en_US/systems/GeneXpert-Family-of-Systems/GeneXpert-Xpress http://www.cepheid.com/en_US/systems/GeneXpert-Family-of-Sys... Brochure (pdf) - https://p.widencdn.net/jdgicj/Cepheid-GeneXpert-Xpress-System-Brochure-US-IVD-0688-English https://p.widencdn.net/jdgicj/Cepheid-GeneXpert-Xpress-Syste... Promo video - https://www.youtube.com/watch?v=lPTHRqDyWC4 https://www.youtube.com/watch?v=lPTHRqDyWC4 About the size of a small laser printer. I'm not clear how it returns results so quickly. I thought that the RT-PCR process required numerous heating and cooling cycles which is what makes it take as long as it does.

vikramkr 7y ago
I looked at their one of their patents and it looks like they might be using something like rolling circle amplification instead of traditional amplification techniques for faster speed (I don't know off sure but it's one of the options in their claims). Kind of like LAMP pcr where you can amplify really quickly to get a signal really rapidly (although the dna at the end isn't really useable for further synthetic biology - it just provides a strong signal). They also mention a couple other types in this patent like strand displacement etc, so there's a lot of options they could be using. Edit: the keyword to look for might be "isothermal" amplification, which means same - temperature amplification. Again, no clue if that's what they're using, I just see that they have patents on using isothermal techniques. These allow for amplifying DNA without cycling the temperature, usually letting the reaction accelerate quickly until a signal is detected, and it can accelerate really quickly sometimes. You know those videos of supercooled liquid water where you bump the bottle and the whole thing freezes? Imagine that you have a situation like that where adding non-coronavirus dna bumps the bottle incorrectly and nothing happens, while adding coronavirus dna makes the whole thing freezes. It's a rapid signal that just gets generated, but often (like with lamp) you just end up with a polymerizated mess that you can't use for DNA engineering in synthetic biology which is why you might use your temp. cycling methods for those uses. Also, they're good for telling you if something is or isn't there, but not so good at telling you how much dna you started with. To figure that out you again use a cycling reaction with the amount of dna doubling each step until it levels out so you know how many doublings happened and can calculate backwards (quantitative rt-pcr, or qPCR). https://patents.google.com/patent/US8900828 https://patents.google.com/patent/US8900828 https://en.m.wikipedia.org/wiki/Rolling_circle_replication https://en.m.wikipedia.org/wiki/Rolling_circle_replication https://en.m.wikipedia.org/wiki/Loop-mediated_isothermal_amplification https://en.m.wikipedia.org/wiki/Loop-mediated_isothermal_amp...
- tyre 7y ago
  Thank you for the informative comment! Your example of the water bottle is perfect
  - vikramkr 7y ago
    Thanks! I was trying to find a universally known example or party trick of something just polymerizing quickly,which I couldn't think of, so went freezing instead (since it looks line if like polymerizing? And I think lots of people have seen those videos showing off that trick). If you want clear, beautiful ice, you've gotta freeze it the right way. But if you want to know if water is cold enough to freeze and don't care about using the ice, bump the supercooled bottle. Trying to convey the differences in constraints between a) detecting dna, where it's a destructive test for all intents and purposes since the end product is just tossed into biohazard - you just wants signal and b) making more usable dna for further research, where you want that end product for further manipulation and so has to high quality, usable dna, not just a polymerized mess. Lots of rapid PCR diagnostics take advantage of this to use gunk-creating rapid tests while scientists working on engineering the same DNA will use temperature cycling processes to clone the DNA and do work on it - each has its use.
andrewon 7y ago
chemistry video: https://www.youtube.com/watch?v=j-y3xi1K7JE https://www.youtube.com/watch?v=j-y3xi1K7JE The fast turnaround time is from integrated sample prep and reagent cartridge. It just uses standard thermocycling PCR. PCR doesn't take long when volume is small and heating surface is large.
milksteak42 7y ago
It's worth nothing that this machine is very low throughput - the larger one only takes 4 samples and you have to use their proprietary disposable cartridges. edit: as pointed out below - the largest of the machines has 80 slots and could probably do 2000/day taking around 45min-1hr/test all in Contrast that with a modern real-time PCR machine which typically has capacity for 96 samples, with some machines able to test 384 or even 1536 at a time. The tradeoff is that those machines take 2-3 hours and the lab needs to do nucleic acid extraction separately. The main advantage of this machine is that it does the nucleic acid extraction and PCR in one cartridge and in ~20 minutes. It's great for clinics and field hospitals but for an established laboratory running hundreds or thousands of tests per day, I'd wager that the standard methods are much cheaper and a bit faster overall.
- mlyle 7y ago
  They have bigger systems--- https://www.cepheid.com/en_US/systems/GeneXpert-Family-of-Systems/GeneXpert-Infinity https://www.cepheid.com/en_US/systems/GeneXpert-Family-of-Sy... It's pretty neat-- they have 1, 2, 4, or 16 slot things that you can slot samples into as you're ready, and they process in the background... or the big robot. It's also neat in that they have combined cartridges to do a couple of influenza detections + RSV in one rapid test (with a different color of fluorescence for each). But you're spot on in that this has a costly consumable (the cartridge)
- mkagenius 7y ago
  What is the false positive rates of this, if 10k people are tested everyday, can we expect 100 false positive everyday?
  - killjoywashere 7y ago
    PCR tends to have great specificity and great in vitro sensitivity. The sensitivity drops off with pre-analytic errors that accumulate in real world testing (wrong collection method, wrong media, wrong swab, etc). So false negatives are the problem. The nice thing is that it catches acute infections even earlier than IgM.
  - 7y ago

by js2 7y ago

vikramkr 7y ago

I looked at their one of their patents and it looks like they might be using something like rolling circle amplification instead of traditional amplification techniques for faster speed (I don't know off sure but it's one of the options in their claims). Kind of like LAMP pcr where you can amplify really quickly to get a signal really rapidly (although the dna at the end isn't really useable for further synthetic biology - it just provides a strong signal). They also mention a couple other types in this patent like strand displacement etc, so there's a lot of options they could be using. Edit: the keyword to look for might be "isothermal" amplification, which means same - temperature amplification. Again, no clue if that's what they're using, I just see that they have patents on using isothermal techniques. These allow for amplifying DNA without cycling the temperature, usually letting the reaction accelerate quickly until a signal is detected, and it can accelerate really quickly sometimes. You know those videos of supercooled liquid water where you bump the bottle and the whole thing freezes? Imagine that you have a situation like that where adding non-coronavirus dna bumps the bottle incorrectly and nothing happens, while adding coronavirus dna makes the whole thing freezes. It's a rapid signal that just gets generated, but often (like with lamp) you just end up with a polymerizated mess that you can't use for DNA engineering in synthetic biology which is why you might use your temp. cycling methods for those uses. Also, they're good for telling you if something is or isn't there, but not so good at telling you how much dna you started with. To figure that out you again use a cycling reaction with the amount of dna doubling each step until it levels out so you know how many doublings happened and can calculate backwards (quantitative rt-pcr, or qPCR). https://patents.google.com/patent/US8900828 https://patents.google.com/patent/US8900828 https://en.m.wikipedia.org/wiki/Rolling_circle_replication https://en.m.wikipedia.org/wiki/Rolling_circle_replication https://en.m.wikipedia.org/wiki/Loop-mediated_isothermal_amplification https://en.m.wikipedia.org/wiki/Loop-mediated_isothermal_amp...

tyre 7y ago
Thank you for the informative comment! Your example of the water bottle is perfect
- vikramkr 7y ago
  Thanks! I was trying to find a universally known example or party trick of something just polymerizing quickly,which I couldn't think of, so went freezing instead (since it looks line if like polymerizing? And I think lots of people have seen those videos showing off that trick). If you want clear, beautiful ice, you've gotta freeze it the right way. But if you want to know if water is cold enough to freeze and don't care about using the ice, bump the supercooled bottle. Trying to convey the differences in constraints between a) detecting dna, where it's a destructive test for all intents and purposes since the end product is just tossed into biohazard - you just wants signal and b) making more usable dna for further research, where you want that end product for further manipulation and so has to high quality, usable dna, not just a polymerized mess. Lots of rapid PCR diagnostics take advantage of this to use gunk-creating rapid tests while scientists working on engineering the same DNA will use temperature cycling processes to clone the DNA and do work on it - each has its use.

andrewon 7y ago

chemistry video: https://www.youtube.com/watch?v=j-y3xi1K7JE https://www.youtube.com/watch?v=j-y3xi1K7JE The fast turnaround time is from integrated sample prep and reagent cartridge. It just uses standard thermocycling PCR. PCR doesn't take long when volume is small and heating surface is large.

milksteak42 7y ago

It's worth nothing that this machine is very low throughput - the larger one only takes 4 samples and you have to use their proprietary disposable cartridges. edit: as pointed out below - the largest of the machines has 80 slots and could probably do 2000/day taking around 45min-1hr/test all in Contrast that with a modern real-time PCR machine which typically has capacity for 96 samples, with some machines able to test 384 or even 1536 at a time. The tradeoff is that those machines take 2-3 hours and the lab needs to do nucleic acid extraction separately. The main advantage of this machine is that it does the nucleic acid extraction and PCR in one cartridge and in ~20 minutes. It's great for clinics and field hospitals but for an established laboratory running hundreds or thousands of tests per day, I'd wager that the standard methods are much cheaper and a bit faster overall.

mlyle 7y ago
They have bigger systems--- https://www.cepheid.com/en_US/systems/GeneXpert-Family-of-Systems/GeneXpert-Infinity https://www.cepheid.com/en_US/systems/GeneXpert-Family-of-Sy... It's pretty neat-- they have 1, 2, 4, or 16 slot things that you can slot samples into as you're ready, and they process in the background... or the big robot. It's also neat in that they have combined cartridges to do a couple of influenza detections + RSV in one rapid test (with a different color of fluorescence for each). But you're spot on in that this has a costly consumable (the cartridge)
mkagenius 7y ago
What is the false positive rates of this, if 10k people are tested everyday, can we expect 100 false positive everyday?
- killjoywashere 7y ago
  PCR tends to have great specificity and great in vitro sensitivity. The sensitivity drops off with pre-analytic errors that accumulate in real world testing (wrong collection method, wrong media, wrong swab, etc). So false negatives are the problem. The nice thing is that it catches acute infections even earlier than IgM.
- 7y ago