Starting Smart: How to Structure an Integrated Supply Chain in Early-Stage CGT Programs
If you’re part of a small, science-first team navigating the world of cell and gene therapy (CGT), your focus is likely on proof of concept, not procurement. But the truth is, decisions made early (before your first patient dose) can have an outsized impact on your ability to scale, meet regulatory demands, and maintain product quality down the line.
For many academic labs, technology spinouts, and early-stage CGT companies, the temperature-controlled supply chain feels like something to figure out later. That instinct is understandable! But when dealing with highly sensitive starting materials and therapies like CGTs, later can quickly become too late.
Whether you’re preparing for first-in-human trials or just beginning to plan for scale, integrated thinking now can spare you time, cost, and complexity later.
What Early-Stage Programs Need to Understand About Building the Supply Chain Foundation
CGT supply chains are fundamentally different from those in traditional pharmaceuticals. Understanding this additional complexity early helps you avoid missteps that can delay or derail your program down the road.
In traditional pharma, drugs are manufactured in bulk, stored in controlled room temperature or refrigerated conditions, and distributed to wholesalers or pharmacies. CGT, however, doesn’t work that way. Therapies are often autologous and patient-specific, requiring individualized manufacturing runs. The distribution process can include direct-to-clinic or even direct-to-patient, and both delivery and turnaround times are far shorter.
Cold chain needs are another key differentiator. Traditional drugs may have months of shelf life at standard temperatures, but CGT products often require cryogenic storage below -150°C, and maintaining the viability of starting materials and efficacy of final drug product depends on precise handling throughout the supply chain.
This is why traceability, flexibility, and Chain of Compliance® are non-negotiables, even as early as Phase I. Small-scale and early-stage operations need the same rigorous standards as commercial therapies, and the foundation you build now affects your ability to scale later. From packaging and labeling to documentation and temperature monitoring, every element should reflect integrated and forward-looking thinking. Even if your current scope is limited to early-phase trials, your choices today shape your ability to meet future demand.
Clinical vs. Commercial: Planning for Both from the Beginning
It can be tempting to focus solely on getting through early-phase trials as quickly as possible. Speed and flexibility are top priorities, and rightly so. But without an eye toward future commercial requirements, you may be building a system that’s not set up to scale when the time comes.
Clinical-stage decisions often prioritize rapid turnaround and workaround-heavy processes. But what works in a Phase I trial with 10 patients can’t always support a global Phase III trial (or commercialization). That’s where problems start.
Take, for example, a startup that designs its manufacturing and logistics processes purely to meet the needs of Phase I trials. There’s no long-term data tracking, no scalable packaging system, and no alignment with commercial regulatory expectations. When that therapy shows promising indications of success and enters later-phase trials, the company has to scramble to redesign processes, requalify expanded shipping lanes, find new vendors who can support expanded cryopreservation or biostorage needs, and look at new shipping system and packaging performance qualifications. This delays progress, increases cost, and introduces risk at the worst possible time.
By contrast, teams who build early systems with later phases in mind can avoid costly rework. That doesn’t mean over-investing before it’s needed, but it does mean choosing partners and processes with intention. Consider your documentation approach, your kit production, your labeling conventions, and your quality standards. Are they acceptable for commercial use?
Planning for commercial scalability from the beginning builds a bridge between your clinical ambitions and your long-term vision. Even small choices, like how you track chain of custody or maintain cold chain integrity, can either accelerate or hinder your path to market. Making smart decisions early can help ensure that your first steps set the stage for success at every stage that follows.
Cryopreservation Strategy for Lasting Impact
One of the most critical decisions you’ll make early on is whether to use fresh or cryopreserved starting material. Fresh cells can be highly sensitive to timing, temperature, and transport logistics. Coordinating apheresis collection, manufacturing slots, and shipping schedules becomes a complex puzzle with tight windows and high risk, and as you expand patient populations over time, the complexity only becomes more of a roadblock.
Cryopreservation of leukapheresis starting material extends your flexibility. It decouples collection from manufacturing, giving you more control over timing and site coordination. It can also enhance consistency, and when done well, cryopreservation of starting materials reduces input variability and provides a more stable foundation for scaling manufacturing.
But consistency is key. Without standardized protocols for collection and collection kits, as well as consistent freezing, storing, and thawing protocols that are followed at every site of care as the patient network expands, variability creeps in. Differences between collection sites or freezing procedures can impact cell viability and potency. That’s why many teams are turning to automated, closed processes for cryopreservation that reduce manual variability and support reproducibility across geographies and time.
Even if you’re only now entering Phase I, it’s worth asking whether your starting materials approach today supports your plans for tomorrow. Is your process scalable across clinical and commercial operations? By laying the groundwork early with a strong cryopreservation strategy, you’re preparing for standardization and scale. A thoughtful approach now can streamline manufacturing, improve product consistency, and ultimately support better outcomes for patients.
Logistics and Quality Partnerships: Choose Early, Choose Wisely
For CGT programs, logistics goes beyond transportation to become an extension of your manufacturing and quality systems. The vendors you choose early matter more than you think.
It’s easy to think of logistics as the final step, moving product from Point A to Point B. But CGT logistics include packaging validation, temperature monitoring, trade compliance, chain of custody, risk mitigation… a truly comprehensive and thorough approach, because cold chain failure can mean product loss – or worse, compromised patient safety.
Quality matters at every touchpoint. For example, shipping systems should be requalified after every use to maintain performance and properly cleaned and validated before every use. Programs like Veri-Clean® ensure the highest level of decontamination, protecting the integrity of shipments. Temperatures and other critical parameters like shock or tilt must be continuously monitored and documented throughout every shipping journey.
Choosing multiple vendors to handle different steps may seem manageable early on, but as complexity grows, so do risks. Disjointed systems lead to gaps in accountability, handoff errors, and audit challenges.
Integrated, end-to-end supply chain partners like Cryoport Systems can streamline the entire cold chain and offer consultative guidance as your program evolves. The right partner can help you design your early systems with scalability in mind, flag risks before they become problems, and adapt as your clinical demands shift.
For example, a true end-to-end supply chain partner can ship collection kits to the collection site, along with the pre-conditioned shipping system to hold the leukapheresis material. Then they can handle transporting the collected material to their cryopreservation facility, cryopreserve the material using a standardized, automated closed process, and move the cryopreserved cells into their onsite, GMP biostorage until it’s time for manufacturing. Then they can transport the material in validated shipping systems to the manufacturing facility, and then from manufacturing all the way to point of care for patient administration. One relationship with one vendor, set up from the beginning to support your program and scalable through expansion into Phase II, Phase III, and eventually commercial distribution. As much or as little support as you need now and in the future, with full risk mitigation and future-proofed compliance strategies from the start.
When it comes to smart cold chain management, think beyond shipping. Do your partners help you anticipate regulatory needs? Can they scale with your program? Are they proactive in identifying weak spots before they break?
Making these decisions early, while your team is still small and agile, can set the tone for a more resilient supply chain that evolves with your program.
How to Move Forward with Practical Next Steps
You don’t need to have all the answers, but you do need to ask the right questions. When planning your supply chain strategy, consider:
- Have you mapped how your early supply chain considerations will support (or constrain) your commercial goals?
- Are your partners and vendors able to scale with you, and do they offer integrated services such as biostorage that streamline your processes?
- Do you have a cryopreservation strategy that works across sites and geographies?
- Are you confident in your packaging, labeling, and documentation approach for future audits?
- Do your logistics partners support not just transport, but also quality, trade, and compliance?
Early-stage CGT programs are full of unknowns, but your supply chain doesn’t have to be one of them. The right partners can help you spot risks, simplify complexity, and build systems that work from first patient to first product launch… and beyond.
You don’t have to be a supply chain expert to make smart early decisions. You just need to know where the risks lie and who can help you avoid them. Building a flexible, compliant, and scalable supply chain now gives your therapy the best chance to succeed later.
Your early team is laying the foundation for something big. With the right guidance and by partnering with experienced supply chain experts like Cryoport Systems, that foundation can support every phase of growth, from a single trial site to global commercialization.
Start smart. Plan early. And remember, the choices you make today are building the future of your therapy.
