Summary: A new digital PCR instrument with two different sample throughput formats (24 and 96), many more partitions, and more colors to enable multiplexing
The digital PCR market continues growing, as it finds its continued utility for absolute quantitation of nucleic acids for a multitude of applications, from rare virus detection in infectious disease to monitoring minimal residual disease in myeloid leukemias with very high sensitivity and specificity, to detecting circulating tumor DNA in what is colloquially called “liquid biopsy”.
A full four years ago I wrote about Formulatrix and their (approximately) 500-partition system in a 96-sample throughput format for quantifying NGS libraries. Now they are readying a full commercial launch of a new system called Constellation®.
Existing digital PCR offerings
Of particular interest is the sample format. At present the market leader is Bio-Rad with what was once called Quantalife technology. The QX200 Droplet Digital has a 96-sample format, which has found wide adoption, with about 20,000 partitions, and Bio-Rad acquired RainDance Technologies RainDrop Plus with 10 million partitions and a 8-sample format. Thermo Fisher Scientific has the QuantStudio 3D also with about 20,000 partitions, but this system is a single-sample instrument.
Another system recently on the market is Stilla Technologies Naica instrument, that is unique in offering a 4-sample/chip format, a three-color system for multiplexing the PCR within the same partition, and integrates droplet formation with the thermal cycling, reducing the hands-on time and simplifying the workflow. It can be argued that not many people use multiplexing for real-time PCR due to the technical difficulty in getting it to work properly; however having the capability of additional amplicons per droplet for multiple targets is an attractive feature.
Constellation’s 24- and 96-sample format
The new Formulatrix Constellation now ups the ante, along several dimensions. There are two sample formats: a 24-sample, 36,000 partition format (for ‘rare detection’ and ‘high CNV’ applications), and a 96-sample, 8,000 partition format (for gene expression, mutation detection etc.) Like Stilla, the instrument will both partition and thermal cycle the samples, using the same polypropylene-based microfluidic gridding technology as the prior 496-partition iteration.
The workflow is straightforward: 5 minutes to pipette samples onto the plate, 1 minute to apply a seal, and 1.5 hours for automated partitioning and thermal cycling. (The Stilla by contrast will take 4 samples/chip and 3 chips per run or 12 samples per run, takes a longer time overall, about 2.5 hours
In addition, Formulatrix has built in five-color detection, and the ability to load up 8 plates at a time (for a total sample throughput of 192 samples at 36K partitioning, or 768 samples at 8K partitioning.
20-fold smaller geometry
Interestingly, with the prior format 96-sample, 496-partition format plate had a volume per partition of 4.4 nL, and is retained as a higher-throughput option (called the ‘CONSTELLATION Digital PCR Modules‘) at 30 plates per hour. For the new system, the partitions are only 0.22 nL in the new 24- and 96-sample plates, or a 20-fold decrease in volume. Quite the decrease there!
Only an instrument, not reagents
It is not uncommon for users of the Bio-Rad QX200 to use other vendor’s PCR master-mixes, although Bio-Rad would warn that users would do so at their own risk. The same is true for the other vendors. However, Formulatrix does not manufacture real-time reagents for digital PCR, and states that it is ‘designed to work with probe based chemistries (for example, Taqman or IDT probe assays). The CONSTELLATION is also compatible with EvaGreen’.
Choices, choices, choices
Formulatrix is upping the ante here: high sample throughput, shorter sample-to-answer turnaround time, minimal hands-on time, and a promised competitive price-point for both the instrument and per-sample cost. It can be easily imagined that having a 24-sample throughput system with 30K partitions may hit a sweet-spot for detection of circulating tumor DNA, especially with the potential to multiplex the assay. This product is currently in early-access testing, with a full commercial launch expected in early 2018.