Digital PCR machine price and what the platform costs to run

Deciding whether it earns its place

1. Identify the question that needs absolute counting. Copy number, rare variant detection at low fraction, and quantification without a reference are where partitioning wins. Routine relative expression is not, and running it there is expensive.
2. Cost per data point, not per plate. Reagents, partitioning consumables and the lower number of samples per run together set the real cost. Compare against the conventional platform on the same experiment, not on list prices.
3. Understand what partition count buys. More partitions extend the upper dynamic range and improve precision at low copy number. The specification that matters is partitions per reaction and their volume reproducibility, not the headline throughput.
4. Optimise the assay before partitioning. An assay with poor separation between positive and negative amplitude will not be reliably classified into partitions. Optimising annealing temperature and primer concentration first is what makes the counting work.
5. Plan the dilution. Partitioned counting saturates when almost every partition is positive. Samples usually need dilution into the countable range, and finding that range is part of the method.

Counting has its own failure modes

Partitioning replaces curve fitting with classification, and classification fails when the amplitude difference between positive and negative partitions is small or when partitions are lost. Both are visible in the raw plots and invisible in the reported concentration.

Look at the partition plots for every run rather than only the summary. It is the equivalent of looking at amplification curves and it catches the same class of problem.

Throughput is the trade

Partitioned platforms run fewer samples per unit time and per unit cost than plate based amplification. For a screening workflow that is decisive; for a small number of high value measurements it is irrelevant.

Model your actual sample flow before buying. The platform is excellent at what it is for and expensive at everything else.

A thermocycler machine, and what the block decides

A thermocycler is bought on its block. Ramp rate sets the cycle time, uniformity across the block decides whether the corner wells match the middle, and the format, 96 well, 384 well, tubes or a gradient block, decides what you can run without a second machine. A gradient block is worth the premium for a laboratory developing assays, since finding an annealing temperature is one plate rather than eight runs. Ask for the uniformity specification and whether it was measured with a calibrated probe set, and check the lid mechanism, which is what fails first.

A gradient thermocycler, and the plate it saves

A gradient block holds a temperature difference across the plate, typically up to twenty or twenty-five degrees between columns, so an annealing temperature series that would take eight runs happens on one plate in one run. For a laboratory designing primers that is the feature that pays for itself, and it is worth checking how the gradient is specified: the stated range, the uniformity within a column, and whether the block reports the actual temperature per column rather than the setpoint. For a laboratory running fixed assays it is a premium for a capability nobody will use.

pcr workstations, and what the enclosure is for

A PCR workstation is a small enclosure with a HEPA filtered downflow and usually an ultraviolet lamp, and its job is to keep amplicon and airborne DNA out of the reaction rather than to protect the operator. That is why it belongs in a room arranged in one direction: reagent preparation, then template addition, then amplification and analysis, with separate equipment and, ideally, separate rooms. The ultraviolet lamp helps with surfaces and does nothing for a pipette barrel, which is what positive displacement or filter tips are for.

digital pcr reagents, and what differs from qPCR

A digital PCR mix is formulated for partitioning: it has to tolerate being split into thousands of droplets or wells, keep the polymerase active at low volume, and give an endpoint signal bright enough to call each partition positive or negative rather than a curve. That is why a qPCR master mix is not a substitute, and why probe chemistry rather than dye chemistry is usual. Restriction digestion of genomic DNA is often part of the protocol, since long DNA spans partitions and distorts the count.

digital colorimeters and what they measure

digital colorimeters measure absorbance at a fixed wavelength against a reagent specific calibration, which makes them cheap, portable and limited to the determinations their reagent systems cover. A spectrophotometer does the same measurement at any wavelength, which is the reason a laboratory has one of each.

A hydrogen generator for sale, and what it replaces

A hydrogen generator for sale is bought to replace cylinders for a gas chromatograph's carrier or detector gas, and it is specified by purity, flow and delivery pressure against every instrument it will feed. It removes cylinder handling and the storage risk, and it adds a water purity requirement and a maintenance schedule.

lc-ms/ms tandem mass spectrometry and what the second stage buys

lc-ms/ms tandem mass spectrometry selects a precursor ion, fragments it and measures the fragments, which is what gives the specificity a single stage instrument cannot: an interference has to share both masses rather than one. That selectivity is why it is the reference technique for quantifying a small molecule in a complex matrix.

Common questions

When is a digital PCR system worth the cost?

For copy number, rare variant detection and absolute quantification without a reference material. For routine relative expression across many samples, conventional real time amplification remains far cheaper per data point.

Does it really remove the standard curve?

Yes, because the readout is a count of positive partitions rather than a comparison to a curve. That is its main advantage, along with better tolerance of some inhibitors.

Why is my partition classification poor?

Usually assay optimisation. Poor amplitude separation between positive and negative partitions is an assay problem, and it has to be fixed before the instrument can classify reliably.

Browse by service class

• Compare Gene synthesis on advertised prices