We use the QX100 (almost identical to the QX200) and are very happy with it. It seems to be quite robust and easy to use from my perspective. We had no trouble requiring service until now and the Bio-Rad staff was always very helpful. Software is convenient and stable. However, the consumables are really expensive, 5 mL master mix ship for 400€ (= 5 x 96 well plate) and you need lots and lots of plasticware.

Both the system are good for use..but i suggest Applies Bio system PCR machine..because of user friendly

Could you give us an idea of how you want to use the system. Although they are both called digital PCR instruments, the technologies are very different. BioRad uses a droplet protocol, where thousands of droplets are created and PCR is done in the droplets. The QuantStudio is a chip-based system, which has a lower number of total reactions, but more flexibility. The QuantStudio is similar to the BioMark System from Fluidigm. Until you know what your use will be, it is difficult to recommend a system.

Dear Mark, thank you for the question. I think the primary use of the instrument will be in the field of gene expression analyses. Notably, we will probably perform panel gene expression scanning (for instance, for 10-15-20 genes) in a low number of samples. So, our experiments will be high-throughput in the sense of number of genes, not samples.

If you have multiple PCR reactions for the same sample, multiplexing might be an option for you. I don't know about the multiplexing capability of the chip-based system (depends on the number of wavelength that can be analyzed), but the QX100 has 2 lines for fluorescence measurement, meaning you can use two different fluorophores in TaqMan PCR (duplex assay).

Hi Peter,

Depending on the amount of multiplexing, I suspect a chip-based solution may be better for you. Although the BioRad system is two-colour, the chip-based systems do not need different colours. Instead, each reaction is done in individual nano-wells. As such, you can multiplex a very large number. The disadvantage of this, is that you are loosing sensitivity of the digital PCR system. For example, suppose a certain system can perform 3000 reactions per chip. Traditional digital PCR would be to do the same reaction 3000 times on the chip, then count the number of positive and negative reactions - That's good statistical power. If, however, you use the chip and run 100 different reactions, then they are only replicated 300 times. I've seen a setup where someone had over 100 different reactions. In this case, the digital PCR system is really only a very high throughput qPCR system, and has lost the biggest advantage of the digital PCR process, which is replication. Still, it may be useful to do this. The BioRad system is perhaps the "purest" form of digital PCR, as you can only multiplex two genes per reaction, but the number of replications is very high (>20 000) per assay.

Thank you Mark and Michael! If I get it right, BioRad system will never allow us to analyze more than one sample and up to two genes in a single run. On the other hand, ABI system is not limited to the pure digital PCR setup, so we can run, for example, single sample with 4 different reactions on a single chip. In the latter case, will we yield high enough statistical power to consider our reaction a digital PCR? Or will we just break the target-per-well distribution allowing the digital PCR absolute quantification?

That is just about right, Peter. Le ABI system was acquired from a company called Biotrove. As far as I can remember, Biotrove never used the term Digital PCR. Rather they claimed to have an "ultra high throughput" PCR machine. At a time where 96 wells was "a few", and a few 384-well systems were on the market, Biotrove was saying 3000 samples. At that time, the goal was either different reactions or different samples. Later, when Digital PCR became a popular theme, the instrument and software were adapted.

In terms of "statistical relevance", I think either instrument is fine. Each instrument will have specific strengths, however. There is no room to get into this here, but you can look at how each instrument operates. Because of the droplet process on the BioRad instrument, it's main advantage will be in giving significant results even when measuring genes that have very different levels of expression. As you know, regular PCR does very poorly in a multiplexe reaction if Gene A is expressed 5 or more times more than gene B. In this case, it is very common that only Gene A will be detected. The BioRad system easily detects 100:1 expression ratios. It's disadvantage is throughput. I'm not certain this really answers your question. At this point, it may be worth getting reps to go present their systems to you.

Mark, thanks a lot! Indeed, we now have a certain vision of the situation so as to address BioRad's and LT's reps.

Hello everyone - I know that this is an old thread, but I think there was some confusion about which dPCR platform Peter was asking about. Mark was speaking about performing digital PCR on our OpenArray plates (each plate has 3072 thru-holes), which is quite different from using our newer QuantStudio 3D instrument (for which each chip has 20,000 reaction partitions). I'd be more than happy address any questions you might have about the system if you're still interested - just respond to this thread to let me know. 

Take care,

Kevin