Q+A with Christina Fan – How she's solving genomics’ biggest counting problem with Countable PCR

Christina Fan, CTO and co-founder of Countable Labs, has spent her career pushing the boundaries of genomics — pioneering work in noninvasive prenatal testing and single-cell sequencing. 

As a genomic technology innovator with recognitions including MIT TR35 and Forbes 30 under 30 (twice!), her focus has been on creating tools for counting molecules accurately and efficiently — because in biology, accurate counting is truth. 

I sat down with Christina to discuss what motivated her to redefine how scientists quantify molecules, why it was such an important problem to tackle, and how that led her to invent Countable PCR. 

Christina, what inspired the creation of Countable PCR – to redefine how scientists quantify molecules?

Christina: For me, it was about addressing the core limitations scientists face with molecular counting. In biology, accurate counting isn’t just helpful—it’s the foundation of truth. But the tools we had were either too convoluted, too slow, or prohibitively expensive when precision was essential. I wanted to change that.

Where did your thinking about this begin?

Christina: While I was a graduate student, I was using the Fluidigm BioMark Digital Array. It was one of the first commercial digital PCR platforms. It was limited to roughly 700 wells per chip. But I needed tens of thousands of molecule counts per sample to get statistically meaningful data. My advisor joked that I should just run a ton of chips because grad student labor was "cheap." It was a joke, of course, but it planted a seed: What if we could generate millions of counts effortlessly from a single tube?

You later explored next-generation sequencing (NGS) as a counting tool. What were the challenges there?

Christina: I turned to NGS to pioneer its early use as a molecular counting tool for non-invasive prenatal testing (NIPT). NGS gave us the scale—we could count millions of molecules—but it came with huge trade-offs. There was amplification bias, massive data volumes, and really intricate workflows. I was also early to incorporate Unique Molecular Identifiers (UMIs) into sequencing methods, particularly for single-cell and spatial sequencing. But, UMIs require deep sequencing coverage, making experiments costly and dependent on complex de-duplication algorithms. A large portion of molecules are inevitably lost during library preparation, and ultimately, reported counts are really only estimates and the sensitivity of picking up rare variants is fundamentally limited.

Was there a particular turning point when you decided a better method for quantifying molecules had to exist?

Christina: Absolutely. I became convinced that we could develop a simpler, more accurate approach. Something that didn’t rely on expensive reagents, custom informatics, or complex algorithms. A method capable of detecting minute differences unmeasurable by qPCR. A method versatile enough to quantify both abundant and rare molecules in the same tube. A method enabling scientists to multiplex many more targets than traditional qPCR or digital PCR without resorting to NGS. That vision drove me to co-found Countable Labs and develop Countable PCR.

What makes Countable PCR different from existing solutions?

Christina: Countable PCR is fundamentally designed to count DNA molecules directly from within a single tube. There’s no need for sequencing, UMIs, or even library prep. There’s no sample loss, no custom algorithms—just pure counts read by a simple benchtop instrument. It’s the simplest, most direct way to measure DNA copies—with an exceptional dynamic range.

It seems like you’re addressing more than just the ability to accurately quantify molecules?

Christina: Yes! Our philosophy at Countable Labs is simple: scientists shouldn’t have to choose between precision and simplicity. They shouldn’t waste time designing workarounds or compensating for limitations in their tools. With Countable PCR, we’re offering a true solution, not a patch. It’s a tool that respects the scientist’s time and the importance of their data. That’s what makes Countable PCR different—and that’s what keeps us pushing forward.