Designing Species- and Strain-specific qPCR Assays
Recently we shared how Branchpoint’s qPCR assays allow you to efficiently quantify your microbiome targets with better limits of detection, speed, and cost – but how do we design them in the first place?
Let’s take a closer look at how we ensure accurate quantification within complex samples.
What’s in a name?
First, you need to clearly define your target. Are you after a species, strain, or SNP?
It might sound simple, but just relying on a name isn’t enough.
Names can change and they don’t tell you who’s related. That’s why we use a proprietary database and evolutionary expertise to precisely define targets.
Next, we get to work on finding suitable genomic fingerprints.
Finding Fingerprints with TaxaPrime™ and TaxaClear™
Some targets have hundreds of members and our assays need to capture them all.
To do this, we created TaxaPrime™ – our software that identifies primer and probe sites across all target genomes.
Next, we need to make sure each set is unique. This is where TaxaClear™ comes in – our software that screens primers and probes against a curated database of thousands of species.
By removing primers and probes that aren’t unique, we’re able to design assays using fingerprints found only in our targets.
Insuring Accuracy: Validating qPCR assays in the real world
Let’s face it, PCR can be unpredictable. Primers and probes that seem perfect on paper may not work as expected.
That’s why we rigorously validate all our assays.
We test each assay against positive controls, dozens of negative controls, and complex communities. We make sure our assays work right out of the box.
We do the hard work up-front so you can quantify with confidence.
Branchpoint Biosciences – Where quality comes standard
Every Branchpoint assay passes an extensive design and validation process to ensure accuracy.
Stay tuned for our next post, where we’ll share some exciting results demonstrating how our assays stack up against other approaches to microbiome profiling.
