Choosing the Right Chemistry: TaqMan vs. Universal Multiplexing

<aside>

Countable PCR supports both traditional TaqMan hydrolysis probe (HP) assays and our proprietary Universal Multiplexing (UM). Keep reading to determine the optimal chemistry for your assay.

</aside>

Comparing TaqMan hydrolysis probes and Universal Multiplexing

With support for both Universal Multiplexing (UM) and TaqMan hydrolysis probe (HP) assays, the Countable platform allows you to choose the chemistry best suited for your budget, timeline, and application. UM assays offer significant advantages, including lower cost, faster oligo synthesis, and significantly reduced hands-on optimization time due to the pre-optimized signal generation. Crucially, UM maintains comparable specificity, sensitivity, and multiplexing capability to HP. The table below details the core features differentiating these two technologies:

Assay type	TaqMan hydrolysis probe	Universal Multiplexing
Specificity	High	High
Sensitivity	High	High
Multiplexing	Yes	Yes
Cost of oligos	High	Low
Oligo synthesis turn-around time	Weeks	Days
Pre-optimized signal generation	No	Yes

Estimated cost of TaqMan hydrolysis probes versus Universal Multiplex

When planning your assays, the oligo cost is often a key factor that can significantly impact your budget and the scalability of your experiments. UM significantly reduces the per target oligo cost, offering substantial savings compared to traditional HP. The following table provides an estimated cost breakdown per target for both HP and UM chemistries:

	TaqMan hydrolysis probe	Universal Multiplexing
Forward primer	$10	$20
Reverse primer	$10	$10
Probe	$400	Not required
Total	$420	$30

Choosing the right chemistry for your assay

Deciding between HP and UM often comes down to what your specific experiment needs – whether that's speed, cost-effectiveness, or assay specificity.

	Typical applications	Key benefits
Taqman hydrolysis probes	- Clinical diagnosis

SNP detection assay
Rare molecule detection | - Ideal for long-term, high-volume assays
Proven performance and high specificity | | Universal multiplexing | - Gene expression analysis
Copy number variation
Targeting variable sequences
High-throughput screening of many samples | - Designed for rapid results to accelerate your assay development
Ideal for quick iteration and testing many targets
Prioritizes cost efficiency
Pre-optimized signal generation reduces optimization time for faster sample processing |

Other assay design considerations

Once you've chosen your assay chemistry, the resources below provide guidance for optimal assay design and performance on the Countable platform.

For UM assays, ensure high-quality multiplexing and prevent primer-dimer formation by performing in-silico analysis with the Countable Labs UM Converter Tool. Find detailed instructions in Designing UM assays with UM Converter.
For HP assays, optimize your assay quality and signal-to-noise ratio by including a probe additive (PA) in your reaction set-up. Find PA design and additional details in Transition existing hydrolysis probe assays to Countable PCR. You can also use the Countable Labs PA designer tool with detailed instructions in Designing probe additives using PA Designer.