A close NGS system. What does it mean? - (Jan/21/2015 )
A medical laboratory nearby just bought an Ion Torrent NGS system. I think it must be PGM. My friend told me they made a mistake by buying Ion Torrent for screening purposes before birth, because the system is a close system. What did he mean by that? I found that with an AmpliSeq kit you can screen 300 genes before a child is born, so the system must work. Is he talking nonsence?
Not sure, but it could be either that there are only limited specific genes to survey with this system, making it closed to any unknown but important genes (as would occur with whole genome sequencing), or that the software or the machine are not easily tinkerable.
Ion Torrent does the same NGS as other machines. But as I seen it is smaller, but from the first seminars I got that its more error-prone than pyrosequencing or ligation-sequencing methods. But is quicker, on the other side.
Closed system could mean, that you need to buy all stuff for it from LifeTech, just simply all of it, also enrichment kits, which could mean you can't use predesigned panels that other companies make. I think Agilent is the most advanced in designing these things, for any NGS sequencer. And they offer also free analysis app with purchase of their products.
If the Ion Torrent is not compatible/doesn't wan't to be compatible with other companies products, that is usually called "close system", it's like open-source vs closed-source software.
But it could mean anything else.
Trof on Wed Jan 21 23:36:43 2015 said:
you need to buy all stuff for it from LifeTech, just simply all of it, also enrichment kits, which could mean you can't use predesigned panels that other companies make.
Yes, I think that's what he was trying to say. Now I remember. We sold Real-Time PCR machines together with this guy about 10 years ago. If we sold LightCycler we had to sell the kits from Roche only. But if we sold Rotorgene, we could sell HBV, HCV or other medical diagnostic kits made by other companies for Rotorgene. Roche was a closed system.
Trof on Wed Jan 21 23:36:43 2015 said:
I think Agilent is the most advanced in designing these things
In fact I learned NGS from a guy who came from Agilent to our lab few years ago. But I see most publications use Illumina for their NGS work. Don't you think Illumina's MiSeq is the most used machine globally?
But LightCycler is NOT a closed system. If you have the machine nothing can prevent you from byuing other reagents or kits or anything. If you have this rule then it's just your rule, not the inability of the real-time machine to fit in some universal criteria. You can put there any master mix you want, and plastics you want (well in general, in this case they are very angry about it, that it may not work properly and damage the machine, not sure if true or not), you can export raw data and analyse somewhere else.. there is pretty much open options.
And Roche even doesn't consider their kits as closed, they have a protocol for their cyclers in the manual, yes, but also a general one. When you buy UPL probes, there is note that they desined the protocol for LC, but it should work fine on any system.
But, if you buy LifeTech qPCR assays, they say they can only guarantee the result only using LifeTech mixes and cyclers and everything.
But NGS is not a cycler, requires a standartised prep and data formats and so, and when a company decides they don't want to share the specs, no-one can make a compatible mix or analysis software. That makes it "closed" more easily. From what I personally think about LifeTech, it wouldn't surprise me if they really pushed the "closed system" stuff on this.
I don't know, we don't have NGS machine and I never personally worked with the NGS data, but from what colleague said, the data analysis and annotations is far bigger problem then technicalities like which NGS machine was used (though, depends sometimes a lot on read lengths and accuracy too).
No, it's different for medical diagnostic kits. In here, the Ministry of Health doesn't easily let you use your own reagents I have been told. They approve some kits and you must use only those kits to detect a disease. You can not use your own mastermix for a patient. But your comments are certainly correct for research and study.
Are there really medical diagnostic kits for NGS? That's not a diagnostic method. At least not something that would be routine certified.
For example Ipsogen kits that our hospital hematology department use four routine screens of MRD, has a set manual where the threshold of qPCR Ct calculation must be set to a mentioned value. But at least they have two protocols for two most used cyclers.
But kits that are certified for IVD are usually not bound to a specific cycler, of course if not manufactured by LifeTech in that case they may be ;)
yes, as I mentioned above, the AmpliSeq Inherited Disease kit detects 300 genes from only 30 ng DNA sample.
I just talked to the doctor who does IVF and is the main person who needs the result of this machine. He says they will do an invasive blactomere selection and will do something like colony PCR and drop the selected cell into the reaction buffer. I am not sure if one blastomere will provide 30 ng of template DNA. I am a little sceptical about this method.
I see, so it's the IVF screening kit. Interesting. It was probably just a matter of time.
I this case yes, the company would definitelly require their sequencer. Because it would be difficult to certify anything as IVD if it needed to work across platforms, even if someone wanted, when NGS have so many very different principles right now.
Now I see why LifeTech was pushing out Ion Torrent even when it has lower specifity compared to their own Solid etc.
They wanted to develop screening kits for it, as IT is less labourable to handle and more suitable for clinical diagnostic labs.
Clever move.