Cell and Gene Therapy (CGT) companies’ SAP landscapes must support patient-specific manufacturing, chain of identity and custody, cold-chain logistics, and rigorous regulatory compliance, often while scaling rapidly from clinical trials to commercial launch. With the global CGT market already exceeding $27 billion and projected to grow at more than 20% CAGR over the next decade, operational scalability has become a board-level concern, not just an IT one.
KEY TAKEAWAYS
SAP Clean Core is an architectural principle designed to keep S/4HANA as close to standard as possible by avoiding modifications to SAP-delivered objects.
For many CGT companies, SAP customizations are turning into technical debt that slows expansion and complicates integration.
Clean Core encourages CGT companies to be more intentional about customization, while enabling better differentiation by placing complexity where it belongs.
Many CGT companies begin by inventorying existing SAP customizations, identifying which still deliver value and which do not.
Against this backdrop, SAP’s Clean Core philosophy is forcing CGT companies to reconsider a long-standing default: heavy customization. What once enabled flexibility may now threaten agility, scalability, upgradeability, and compliance in an industry where change is constant. Clean Core, however, does not require CGT companies to abandon differentiation entirely. It simply requires them to move it out of the ERP core and into architectures that can evolve as quickly as demand.
Below, we explore what Clean Core really means for the industry and when companies should prioritize standardization vs. customization.
SAP CLEAN CORE FOR CGT
SAP Clean Core is an architectural principle designed to keep S/4HANA as close to standard as possible by avoiding modifications to SAP-delivered objects. Instead, differentiation is achieved through configuration, in-app extensibility, APIs, events, and side-by-side extensions, most commonly on SAP Business Technology Platform (BTP).
For CGT companies, this approach aligns directly with regulatory realities. Custom code embedded in the core often increases validation scope and complicates change control, significantly raising the effort required to maintain a validated state during upgrades. In contrast, cleaner cores allow organizations to isolate changes and adopt SAP innovations more predictably, which is an increasingly important capability as SAP accelerates its cloud release cadence.
SAP CUSTOMIZATIONS FOR CGT
CGT manufacturing models were never designed for traditional ERP assumptions. Patient-specific batches challenge standard lot structures, and chain of identity and custody requirements stretch conventional serialization logic. Furthermore, integration with LIMS, MES, clinical systems, and external logistics partners often demands sophisticated orchestration.
As a result, many CGT companies turned to SAP customizations to “make the system fit.” While effective in early clinical or pre-commercial stages, these solutions often encode assumptions optimized for low volumes and manual oversight.
As the industry matures—now supporting over 3,000 active cell and gene therapy clinical trials globally—those assumptions begin to break. What once enabled speed becomes technical debt that slows expansion and complicates integration.
KEY CONSIDERATIONS MOVING FORWARD
Clean Core Does Not Mean “Standardize Everything”
A common misconception is that Clean Core forces CGT companies into rigid, one-size-fits-all processes. In reality, Clean Core enables better differentiation by placing complexity where it belongs.
Core ERP capabilities, such as financials, procurement, inventory valuation, and baseline quality management, rarely provide competitive advantage in CGT; these processes benefit from standardization, especially given auditability and compliance requirements.
Differentiation, however, remains essential at the edges. Patient orchestration, advanced scheduling, therapy-specific release logic, and complex partner integrations can (and should) be implemented as modular extensions. SAP itself positions Clean Core as a way to reduce core customizations by as much as 80%, while still enabling innovation through approved extensibility frameworks.
The result is not less flexibility, but flexibility without fragility.
Regulatory and Validation Implications
SAP architecture decisions for CGT companies are inseparable from validation strategy. Custom code inside the SAP core typically requires full validation cycles for upgrades, patches, and even minor changes. Side-by-side extensions, when properly designed, can be validated independently, significantly reducing validation scope and accelerating release cycles.
This distinction matters as regulators continue to expand pathways for advanced therapies. The FDA and EMA are approving CGT products at an increasing pace, placing pressure on manufacturers to scale operations without introducing compliance risk. Clean Core architectures help organizations stay aligned with both regulatory expectations and SAP’s innovation roadmap.
Be Deliberate About Customization
Clean Core is not a blanket prohibition on customization. Instead, it encourages CGT companies to be more intentional about customization, evaluating customization decisions through two lenses: regulatory necessity and business differentiation.
For example, if a customization exists primarily to compensate for legacy process design, it may be a candidate for retirement, or if it enables patient safety or therapy viability, it may be justified (but should still be externalized from the core when possible).
Leading CGT organizations establish these guardrails early, particularly during S/4HANA transformations or commercialization readiness initiatives.
Organizational Change
The most significant barrier to Clean Core adoption is rarely technical. It is organizational. Business teams accustomed to embedding logic in SAP must adapt to product-oriented thinking. IT teams must evolve from ABAP builders to platform architects, and quality and validation teams must grow comfortable with modular, service-based landscapes.
Many CGT companies begin by inventorying existing SAP customizations, identifying which still deliver value and which do not. This exercise often becomes a catalyst for broader operating model change.
FINAL THOUGHTS
The goal of SAP Clean Core for CGT is not to limit capabilities, but to instead ensure that SAP systems can keep pace with scientific progress and market growth. By pairing a standardized SAP core with well-governed, modular extensions, CGT organizations can maintain compliance and scale operations.
