High-resolution and precise genome integrity in three days – no bioinformatics needed

When genome integrity is on the line, time and clarity are everything.

If you’re using digital PCR (dPCR) to confirm vector integrity, you’ve likely hit a wall: multi-target linkage analysis takes weeks. Worse, it’s powered by assumptions — statistical models like Poisson distribution and Monte Carlo simulations — that introduce ambiguity.

Countable PCR changes all of that. It delivers high-resolution linkage analysis in just three days – no bioinformatics, no mathematical gymnastics, no guessing.

Skip the statistical assumptions

With dPCR, confirming genome integrity requires estimating co-localization using complex statistical formulas and occupancy models. The software essentially guesses how many partitions might contain a fully linked sequence, versus fragments that happened to land in the same well.

This means the result isn’t what’s observed — it’s what’s inferred.

Countable PCR is different. Using a structured gel-like matrix with ~30 million compartments, it physically separates single molecules before amplification. After PCR, the system simply counts which compartments contain all the regions you’re looking for — no threshold tuning, no λ (lambda) estimates, no Poisson corrections.

You see the actual signal – no math or assumptions required.

Multiplexing that’s faster and cheaper

With Countable’s Universal Multiplexing Kit, you amplify multiple targets using standard primers with universal adapters. That means:

No custom TaqMan probe design
No probe optimization phase
Rapid iteration and lower cost per assay

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In one case study, researchers targeted three plasmid regions — CMV enhancer, GFP, and poly-A. The Countable System generated composite images from three channels and reported exact counts of full-length and partial sequences — seen in the figure above. A white signal is all three regions — intact and linked. Two colors or fewer means partial genome.

The best part, it took just 3 days from designing this experiment and ordering primers to seeing the results.

Simple, direct, and visual.

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Written by Stefanie Kall

Stefanie Kall, PhD is Sr. Staff Product Manager at Countable Labs, where she works closely with customers to support the development of Countable PCR technology. She earned her B.S. in Biochemistry from (The) Ohio State University, her M.S. in Biotechnology from Northwestern University, and her Ph.D. in Biochemistry and Molecular Genetics from University of Illinois at Chicago.

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Before Countable Labs, Stefanie worked in the commercial and product marketing space for Nanotemper Technologys and Avantor.

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When she’s not writing application notes or perfecting slides, she’s found reading books in the company of her cat Laszlo and dog Ada.

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