Direct comparison
Digital PCR vs qPCR: Absolute Quantification
Digital PCR counts partitions for absolute copy number; qPCR needs a standard curve. When dPCR is worth it: rare alleles, copy number, inhibited samples.
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How do qPCR, Digital PCR compare side by side?
The table below compares qPCR, Digital PCR across 11 procurement-relevant dimensions, from measurement principle through reporting guideline.
Side-by-side comparison
| Dimension | qPCR | Digital PCR |
|---|---|---|
| Measurement principle | Real-time kinetic — Cq/Ct read against a standard curve | End-point, statistical — positive/negative partitions counted, Poisson-corrected |
| Standard curve required | Yes, for absolute quantification | No — quantification is intrinsically absolute |
| Typical dynamic range | ~7–8 orders of magnitude in one run | A few orders of magnitude, set by partition count |
| Precision at low copy number | Degrades near the detection limit (Cq scatter) | Strong — Poisson-limited but stable down to single molecules |
| Sensitivity to amplification efficiency | High — curve fit assumes near-100% efficiency | Low — end-point positive/negative call is efficiency-tolerant |
| Tolerance to PCR inhibitors | Lower — inhibition shifts Cq, biasing quantity | Higher — inhibition affects individual partitions, not a shared threshold |
| Rare-allele / low-frequency mutation detection | Poor without added enrichment chemistry | Strong — partitioning physically separates rare variant from excess wild-type |
| Copy number variation calling | Workable, needs replicates to resolve small differences | Direct count ratio — more reliable integer copy calls |
| Throughput / turnaround | High — 384-well plates, fast cycling | Lower — partitioning adds a step, fewer samples per run |
| Per-sample cost | Lower — ubiquitous instruments and reagents | Higher — specialised partitioning consumables |
| Reporting guideline | MIQE | dMIQE (digital MIQE) |
Common questions
Common questions about qPCR vs Digital PCR
Can digital PCR replace qPCR entirely?
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No. For high-throughput screening, wide dynamic range in a single run, or routine relative gene-expression work, qPCR is faster and cheaper. dPCR is worth the added cost specifically where absolute copy counts, rare-variant detection or inhibitor tolerance matter more than throughput.
Does digital PCR need a standard curve?
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No — that is its main structural advantage. Counting positive and negative partitions and applying Poisson statistics gives an absolute copy number directly, without calibrating against a curve of known standards the way qPCR’s Cq-based quantification requires.
What is dMIQE?
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dMIQE (digital MIQE) is the reporting-guideline extension for digital PCR experiments, parallel to the MIQE guidelines for qPCR. It specifies what should be reported: partition count and volume, the fraction of positive partitions, the Poisson correction applied, and how ambiguous (“rain”) partitions were thresholded.
Going deeper
