Industry case: SciLifeLab infrastructure essential for Countagen to develop a same-day analysis kit for gene editing

SciLifeLab’s CRISPR Functional Genomics (CFG) infrastructure unit has played an essential role in aiding the development of GeneAbacus, a ready-to-use gene editing analysis kit soon to be launched by the start-up company, Countagen. The kit aims to reduce the time and resources needed to analyze gene editing efficiency and specificity. Using the infrastructure available at SciLifeLab, the company has benefitted from a test environment and expert advice in order to benchmark their product against current protocols.

“At the moment, we are addressing academic researchers who regularly use CRISPR to modify genes in cultured cells or model organisms to study basic cell biological processes or develop new therapies. Going forward, we plan to develop a higher throughput version suitable for the demands of larger pharma and biotech companies”, says Felix Neumann, CEO and co-founder of Countagen.

The CRISPR Functional Genomics (CFG) infrastructure unit has been instrumental in various aspects such as providing access to high-end technology, offering expertise, validating tests, and supplying test batches for Countagen to utilize during product development.

“We make these kinds of gene edits all the time, so we have a lot of material to enable Countagen to test their product. To benchmark Countagen’s kit against one of the current gold-standard methods, we use our digital droplet PCR (ddPCR) system. We’ve trained Countagen staff in ddPCR and its interpretation so they can use CFG’s instrument for validation”, says Bernhard Schmierer, head of the SciLifeLab CFG infrastructure unit.

The GeneAbacus kit aims to decrease the time required to analyze how well a CRISPR manipulation has performed, for example, by quantifying the percentage of cells in a gene-edited cell population that have the desired gene edit within a single day and without the need for expensive instruments or reagents.

“Saving time is a key selling point for us as our technology enables same-day gene editing analysis. Researchers often use multistep workflows for the analysis of pools and subsequent clonal selection, but, ideally, they can now use just one workflow – saving time and material costs. While ddPCR can be tricky and require optimization, and sequencing workflows can be complex and time-consuming, we will offer a ready-to-use kit for in-house analysis. With improved precision and sensitivity, and requiring only standard laboratory equipment, our objective is to provide a tool that rapidly delivers actionable results thereby accelerating gene editing research and development” says Felix Neumann.

Bernhard Schmierer and his team have also taken on the role of users, providing valuable feedback on the overall quality of the product. Most of the labwork in this collaboration is done by Anneke Navis at CFG.

“CFG acts as a testbed for Countagen’s kit. We examine whether the product works as claimed and is user-friendly. It’s crucial that someone not involved in the development can easily use it. We can provide feedback on these aspects. We evaluate the entire kit and, if we encounter unclear instructions or issues, we can address them,” says Bernhard Schmierer.

Countagen presented the GeneAbacus offering at the “CRISPR as a research tool in cancer and regenerative medicine” symposium organized by CRISPR Functional Genomics, taking place between May 25 – 26 (2023), at Karolinska Institutet. They hoped to attract early access customers and establish collaborations.

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