In the strictly regulated world of biopharmaceutical manufacturing, innovation faces a massive hurdle: the industry inherently hates risk.
In Chemistry, Manufacturing, and Controls (CMC), deviating from proven, traditional methods can trigger regulatory delays, filing re-submissions, and millions of dollars in lost revenue. Yet, a quiet revolution is taking place in quality control (QC). Companies are finally moving away from slow, decades-old animal assays and traditional PCR in favor of Next-Generation Sequencing (NGS).
In an episode of the Flot.Bio Show, Jean-François Brepson, CEO of PathoQuest, mapped out how this technology is transforming industrial bioproduction. From speeding up viral safety assessments to changing how we validate advanced therapeutics, NGS is rapidly becoming the new gold standard on the factory floor.
1. Shifting from the Lab to the Factory Floor (GMP)
NGS has been a staple of academic research and discovery for years, but its integration into industrial manufacturing required a massive leap. PathoQuest, which spun out of the prestigious Institut Pasteur in Paris, decided to completely pivot its business model from diagnostics to focus on the rigid world of biopharma production.
To change biopharma manufacturing, a technology cannot just operate in an R&D bubble. It has to become fully GMP-certified (Good Manufacturing Practice).
By building a standardized, regulated pipeline around sequencing data, it is now possible to introduce NGS directly into the manufacturing testing loops for clinical and commercial drug phases—a space where the rules of quality control are brutally strict.
2. The Hardware Agnostic Approach: “Intel Inside”
One of the key reasons NGS is scaling so quickly across biopharma manufacturing is that the leading service providers aren’t trying to reinvent the wheel. Instead, they approach sequencing like computer makers use Intel chips—utilizing platforms from industry giants like Illumina and Oxford Nanopore.
The real transformation in biopharma manufacturing comes from how different sequencing architectures are applied to specific manufacturing bottlenecks:
- Viral Safety Testing (Short-Read)
When testing biopharmaceuticals for accidental viral contamination during the production cycle, short-read sequencing (primarily Illumina) provides the extreme depth and accuracy needed to catch microscopic contaminants. - Genetic Characterization (Long-Read)
For advanced therapies, such as modified gene therapies, manufacturers must ensure their genetic mapping is completely accurate. Long-read sequencing (primarily Oxford Nanopore) allows teams to look at the big picture and characterize the entire genetic construct safely.
3. The Death of Animal Testing in Biopharma QC
Perhaps the most disruptive way next-gen sequencing is changing biopharma manufacturing is by entirely replacing traditional in vivo (animal) testing.
Historically, validating the viral safety of a biological batch meant injecting cell-line samples into hundreds of mice and waiting weeks for symptoms to develop. It is a slow, expensive, and ethically fraught process.
NGS changes the math entirely:
- Unprecedented Speed: Turning a multi-week animal assay into a data-driven process that yields results in days.
- Data Robustness: Delivering deep genetic insights that traditional PCR or animal observations simply cannot match.
- Ethical Manufacturing: Fulfilling a massive industry-wide push from global pharma companies looking to completely eliminate animal testing from their routine commercial manufacturing lines.
4. The Regulatory Green Light
An innovative technology can be brilliant on paper, but if regulatory bodies reject the data, it will never change the manufacturing landscape. Fortunately, the wind is at the industry’s back.
Major global regulators—including the FDA, EMA, and the International Council for Harmonisation (ICH)—have evolved their guidelines year after year to actively support and endorse the use of NGS in the QC and manufacturing space.
With regulatory validation and peer-reviewed data now firmly established, next-gen sequencing is no longer just an alternative method. In many modern bioproduction loops, it has officially become the technology of choice.
Watch the full clip:
Jean-François has more than 20 years of pharma leadership under his belt. Before his ten years at PathoQuest, he was a Senior Vice-President in charge of Ipsen’s GI-oncology and endocrinology franchise. This blog is based on the full interview with him, which you can find here: https://flot.bio/episode/jean-francois-brepson-pathoquest-cmc/
