How to Choose a Digital PCR System: 10 Questions to Ask
A practical checklist for labs comparing digital PCR instruments.
Buying a digital PCR system is a significant investment. The right choice depends less on headline specifications and more on how well the instrument fits your assays, sample volume and team. These ten questions help you compare systems objectively.
1. What will you measure?
List your applications for the next three years: rare mutations, copy number, gene expression, pathogen load, vector copy number, or protein biomarkers. Applications decide the channels, partitions and modalities you need.
2. Chip-based or droplet-based partitioning?
Droplet systems emulsify the sample in oil; chip systems create partitions in a fixed microfluidic structure. Chip designs that seal partitions – for example by solidifying the oil phase – avoid droplet fusion and transfer steps. Ask each vendor for the effective partition ratio and partition uniformity, not only the theoretical number.
3. How many partitions per sample?
More partitions widen dynamic range and improve precision. Around 20,000 per sample suits most work; high-density chips of about 60,000 help at the extremes.
4. How many colour channels – and can it multiplex beyond them?
Each channel adds a dye. Ultra-multiplex technology encodes targets by signal combinations, allowing up to 63 targets on a 7-channel instrument. If you plan panels, this matters more than any other specification.
5. Throughput and flexibility
Check samples per run, the minimum run size and how consumables scale. A system that runs from 2 to 24 samples with one chip per sample avoids pooling and waste when sample numbers vary.
6. Time to result and hands-on time
Compare the full process – partitioning, amplification, reading and analysis. Fully automated all-in-one systems can deliver results in three hours or less with only a few minutes of loading.
7. Reagent compatibility
Closed systems lock you into one reagent supplier. Systems compatible with most commercial master mixes make it easier to transfer existing qPCR assays and to control running costs.
8. Sensitivity, accuracy and dynamic range
Ask for specified sensitivity (for example 0.01%), dynamic range (for example 5 logs) and quantification accuracy (for example ±10%), and how they were measured.
9. Software and data integrity
Look for automatic per-channel analysis, adjustable thresholds, 1-D and 2-D plots, export options and, if you work under quality systems, an audit-trail option.
10. Total cost of ownership and support
Ask for a quotation that includes chips and reagents for a realistic annual volume, installation, training, warranty, power supply and shipping. Running cost per sample often matters more than the instrument price.
Checklist summary
| Question | What to check |
|---|---|
| Applications covered | dPCR only, or dPCR + isothermal + immunoassay? |
| Partitioning | Chip or droplet; effective partition ratio; uniformity |
| Partitions per sample | 20K standard; 60K high-density option? |
| Channels / multiplex | Number of dyes; ultra-multiplex capability |
| Throughput | Samples per run; minimum run size |
| Speed | Total time; hands-on time |
| Reagents | Open or closed; dedicated kits available? |
| Performance | Sensitivity; dynamic range; accuracy |
| Software | Analysis tools; audit trail |
| Cost & support | Consumables per year; training; warranty |
Common mistakes when buying a digital PCR system
- Comparing theoretical partition numbers only. What matters is how many partitions are usable. Ask for the effective partition ratio and uniformity, and for example data from an assay similar to yours.
- Ignoring the minimum run size. If a run needs a full plate or cartridge, small batches become expensive. Systems that run from 2 samples with one chip per sample keep the cost per result predictable.
- Underestimating consumable costs. Over five years, chips and reagents usually cost more than the instrument. Build a yearly consumables budget into the comparison.
- Buying fewer channels than your roadmap needs. Upgrading later is often impossible or costly. If panels are likely, plan for 6–7 channels or ultra-multiplex capability now.
- Forgetting the people. Hands-on time, software usability and training determine whether the instrument is used every day or sits idle.
What to ask for in a demo or evaluation
Bring one of your own assays and samples, ideally including a low-abundance target. Ask the supplier to run a dilution series and a no-template control, and review the 1-D and 2-D plots together. Check how thresholds are set, how results are exported and how long each step takes from opening the sample tubes to the final report. If remote evaluation is the only option, ask for raw data files from a comparable assay so your team can review the analysis themselves.
Finally, confirm practical details before ordering: power supply and plug type, bench space (width, depth and height), installation and training arrangements, warranty terms, and how quickly chips and reagents can be resupplied to your country.
How our systems answer these questions
The CY-PCR-02 chip digital PCR system runs 24 samples per run (minimum 2), offers 2 to 7 channels with up to 63-plex quantification, more than 20,000 partitions per sample with ≥98% effective partitions, 0.01% sensitivity and results in three hours or less. The CY-PCR-03 multi-modality system adds digital isothermal amplification and digital immunoassay on the same platform. Both are supplied with chips and consumables and reagent kits on one quotation.
New to the technology? Start with digital PCR vs qPCR, or browse the digital PCR systems overview.
FAQ
How many fluorescence channels do I need?
For single-plex or duplex assays, 2–4 channels are enough. For panels, choose 6–7 channels or a platform with ultra-multiplex capability.
Chip or droplet digital PCR?
Chip systems fix partitions in a microfluidic chip and usually offer a more automated workflow; droplet systems may need more handling steps. Compare partitions per sample, effective partition ratio and hands-on time.
What partition number is sufficient?
Around 20,000 partitions per sample covers most applications; high-density chips (about 60,000) extend precision at very low or high concentrations.
What should a digital PCR quotation include?
Instrument configuration, software, installation and training, chips and reagents for your expected volume, warranty, power supply and shipping terms.
Can one system also measure proteins?
Multi-modality platforms add digital immunoassay, enabling fg/mL protein quantification with matched kits on the same instrument.
Talk to us about digital PCR
Send your application, sample numbers and target list – we recommend a configuration and reply with a written quotation.