Throughput: How Many Samples Can Be Processed With hpPCR Per Day?

In routine laboratory environments, the value of a molecular technology is not determined only by analytical performance. Operational throughput matters just as much.

Laboratories must balance multiplexing capacity, turnaround time, and the number of samples that can realistically be processed in a working day. Platforms that deliver high precision but low daily throughput often struggle to integrate into real workflows.

Hyperplex PCR (hpPCR) was designed with this balance in mind.

Standard Plate Formats Enable Scalable Throughput

hpPCR operates in standard SBS plate formats commonly used across molecular laboratories. With hpPCR, it is possible to process the following sample volumes per day:

• 95 samples + 1 control sample in a 96-well plate.

• 383 samples 1 control sample in a 384-well plate.

96-well plates represent the typical workflow configuration. With hpPCR’s molecular counting approach, each well can generate up to ~1 million total counts, supporting highly precise quantification across many targets.

Because each well supports up to 100 targets, a single 96-well plate corresponds to:

9,600 single-plex measurements in one run.

For laboratories requiring even higher throughput, hpPCR can also operate in 384-well plates. In this format, each well typically supports up to ~300,000 total counts, which is sufficient for genotyping and many high-precision applications, or for even more demanding applications where mid-range multiplex of up to ~30-plex is needed. The economics of hpPCR also make full sense for lower-plex applications in the single digits space.

A full 384-well plate therefore corresponds to:

38,400 single-plex measurements in a single plate.

This combination of multiplexing and plate density allows laboratories to scale throughput depending on their application requirements.

Flexible Imaging Balances Precision and Speed

After amplification, several millions of hpPCR products are generated and are quantified through imaging of the amplification products.

Imaging time is typically 2–5 minutes per well, depending on the number of counts required. The system dynamically adjusts the imaged area based on the target count depth needed for the application.

Applications requiring extremely high sensitivity or quantitative precision will collect more counts, resulting in slightly longer imaging times. Applications such as genotyping or presence/absence detection typically require fewer counts and therefore image faster.

In most use cases, 100–2,000 counts per target provides an effective range depending on the precision required.

Designed for Routine Laboratory Operation

Importantly, the workflow integrates seamlessly with standard laboratory infrastructure.

The imaging systems accept standard SBS plates and perform fully automated autofocus and scanning. In practice, the workflow is straightforward:

Load the plate

Select your samples

Start the run

The system automatically handles the remaining steps, allowing laboratories to process plates with minimal operator intervention.

Multiplexing Changes the Throughput Equation

When evaluating throughput, it is important to consider not just the number of wells processed per day, but the total number of measurements generated per run.

Because hpPCR measures up to 100 targets per well, each plate effectively represents thousands of individual molecular assays.

This fundamentally changes the throughput equation: instead of scaling assays by running more reactions, laboratories scale throughput by extracting more information from every reaction.