When Process Defines the Product: Managing Comparability in Cell and Gene Therapy Manufacturing

Key Takeaways

• Manufacturing changes in cell and gene therapy carry direct clinical and regulatory risk, with inadequate comparability data potentially leading to clinical holds and invalidation of pivotal trial results.

• Regulatory flexibility for comparability narrows as CGT products advance from early development to pivotal trials and commercialization, making late-stage process changes especially challenging.

• Cell- and tissue-based therapies fall outside traditional biologics comparability frameworks, due to inherent biological variability and limited statistical power from small batch sizes.

• Real-world regulatory reviews of genome editing, CAR-T, and gene therapy products show intense scrutiny of site transfers, scale-up, potency assays, and analytical strategies.

• For CDMOs, comparability has become a form of regulatory risk management, requiring early planning, robust change control systems, and platform analytics that span development through commercial manufacturing.

Comparability, in regulatory terms, refers to demonstrating that a manufacturing change has not adversely affected a product’s quality, safety, or efficacy. This principle is the foundation of life cycle management for all regulated biologics, but it carries heightened significance for cell and gene therapy (CGT) products because manufacturing processes are more tightly intertwined with clinical performance. In contrast to traditional biologics, where comparability is often treated as a structured extension of scale-up and process optimization, CGT comparability must contend with living systems, complex biological inputs, and evolving manufacturing platforms. As a result, a change in process is not merely a technical adjustment; it represents a potential change in the product itself.

Manufacturing changes are especially common in the early development of advanced therapy medicinal products (ATMPs), when sponsors are still refining production methods, analytical assays, and control strategies. Regulatory authorities recognize this developmental reality but also make clear that tolerance for uncertainty decreases as programs advance. The acceptable level of flexibility is progressively reduced from non-clinical development through exploratory trials and into pivotal clinical use, reflecting the increasing reliance on accumulated clinical evidence to support safety and efficacy. What may be manageable as exploratory manufacturing evolution in early stages becomes a potential regulatory liability once a product approaches confirmatory trials.

A central reason for this heightened sensitivity is that ATMPs fall outside the formal scope of ICH Q5E, the international guideline that governs comparability for biotechnology-derived medicinal products.¹ While ICH Q5E provides a well-established framework for assessing changes in conventional biologics manufacturing, regulators note that its underlying assumption of highly similar products is particularly difficult to apply to cell- and tissue-based therapies. These products are characterized by inherent biological variability, complex functional attributes, and manufacturing processes that can directly influence clinical behavior. In this context, comparability in CGT cannot be treated as routine scale-up or process transfer; instead, it becomes a fundamental question of whether the post-change product can still be considered the same therapy from a regulatory and clinical perspective.

The U.S. Food and Drug Administration (FDA) explicitly links manufacturing changes in CGT products to clinical risk, positioning comparability as a prerequisite for continued clinical development rather than a purely technical exercise. The agency warns that manufacturing changes made without adequate comparability data can trigger regulatory intervention, including the possibility of a clinical hold. This risk is not confined to a particular phase of development; the FDA may place a study on hold at any stage if a change has the potential to adversely affect safety or effectiveness or if the available evidence does not sufficiently demonstrate that the post-change product remains comparable to the pre-change version.^2–4

The FDA further emphasizes that comparability failures have direct implications for the usability of accumulated clinical data. If analytical, nonclinical, or other supporting evidence cannot establish comparability, the clinical experience generated with the pre-change product may be considered insufficient to support a Biologics License Application (BLA) for the post-change product. In such cases, sponsors are expected to engage with the agency regarding the need for additional clinical investigations rather than assuming continuity of the development program.²

The agency illustrates this risk with a phase III scenario in which both pre-change and post-change manufacturing lots are used within a single pivotal study. If those lots are not shown to be comparable and the sponsor does not provide evidence demonstrating that the change has not affected product performance, the FDA may judge the study design to be clearly deficient in meeting its stated objectives. In this framing, comparability is not an abstract quality concept but a condition for the scientific validity of confirmatory trials themselves.²

The European Medicines Agency (EMA) adopts a similarly risk-based but explicitly stage-dependent view of comparability for ATMPs. In early phases of development, regulators acknowledge that full comparability is not expected when manufacturing processes evolve. Instead, sponsors are required to provide analytical data supporting the linkage between nonclinical safety material and early clinical batches, ensuring that emerging products remain representative of those initially tested. As development progresses, however, expectations shift toward a comprehensive comparability exercise encompassing in-process controls, release testing, and extended characterization assays.⁵

EMA also cautions against introducing substantial manufacturing changes during pivotal clinical studies. Such changes are not recommended because of the complexity of the resulting comparability assessment and the potential impact on the acceptability of clinical data used to support marketing authorization. When late-stage changes are unavoidable, the agency advises sponsors to seek scientific advice to ensure that regulatory expectations are clearly aligned with development strategy.⁵

Across both agencies, a consistent theme emerges: regulatory flexibility narrows as products move closer to confirmation of safety and efficacy. What may be tolerated as developmental evolution in non-clinical or early clinical phases becomes increasingly constrained as the burden of evidence for comparability grows. This progression reinforces the central regulatory message that comparability in CGT is not a static requirement but a dynamic obligation that intensifies across the product life cycle, with direct consequences for trial continuity and eventual approval.⁵

Cell- and tissue-based therapies present comparability challenges that differ in kind, not merely degree, from those encountered with conventional biologics. Regulatory authorities note that these ATMPs fall outside the scope of ICH Q5E because the core assumptions underlying that guideline —the ability to define and reproduce a highly similar product through analytical characterization — are particularly difficult to apply to therapies built on living cells and complex biological systems. Inherent variability, multifactorial functional attributes, and sensitivity to manufacturing conditions make it challenging to demonstrate that a product produced after a process change is meaningfully equivalent to its predecessor.⁵

These scientific realities are compounded by practical constraints in development programs. For many CGT products, especially those targeting rare diseases or produced from limited donor material, the number of available manufacturing lots can be very small. When combined with high lot-to-lot variability, this scarcity undermines the statistical power of analytical and functional comparisons intended to support a comparability exercise. Under such conditions, even well-designed studies may struggle to distinguish true process-related differences from background biological variation, increasing regulatory uncertainty and the risk that comparability cannot be convincingly established.²

Vector-based gene therapy occupies an intermediate position between traditional biologics and cell-based therapies. Regulators acknowledge that these products can, in some cases, be evaluated using principles drawn from ICH Q5E, provided that a careful and robust analytical strategy is applied. This reflects the fact that viral vectors, while biologically complex, can often be characterized using defined physicochemical and functional assays that support a more structured assessment of manufacturing changes.⁵

Even within this category, however, comparability is not routine. The need for extensive analytical characterization underscores that alignment with biologics frameworks is conditional rather than automatic. Vector-based products may resemble biotechnology-derived medicinal products in certain quality attributes, but they remain subject to the broader challenges of CGT development, including sensitivity to upstream and downstream process modifications and the critical role of potency and functional testing in defining product identity.

Genome editing therapies introduce an additional layer of complexity by directly modifying DNA at specified locations within human somatic cells, either outside the body (ex vivo) or within the patient (in vivo). Regulatory definitions emphasize that these products are distinguished not only by their delivery systems but by their intended molecular effect on the genome itself, which places extraordinary importance on control of design, manufacturing, and testing parameters.⁶

To support investigational use, FDA requires that sponsors provide detailed information in their Investigational New Drug (IND) applications covering product design, manufacturing processes, analytical testing, nonclinical safety assessments, and clinical trial design. This breadth of required information reflects the agency’s recognition that genome editing products cannot be evaluated solely through traditional quality metrics. Instead, comparability for these therapies must integrate manufacturing consistency with assurance that genomic alterations remain predictable and controlled across development stages.⁶

The FDA approaches comparability in CGT not simply as a demonstration of sameness but as an exercise in structured risk management. The agency recommends applying a systematic quality risk management framework to identify, assess, and mitigate risks introduced by manufacturing changes. This approach is intended to support a risk-based evaluation of whether a change could affect critical product attributes and by extension patient safety or therapeutic effectiveness.^2,7

At the same time, the FDA acknowledges that risk identification and mitigation are inherently more difficult for CGT products than for conventional biologics. Manufacturing changes may introduce effects that are not readily predictable through standard analytical testing, and uncertainty remains about how best to control or compensate for those risks once they are recognized. This combination of scientific complexity and limited historical experience means that sponsors must often make comparability decisions with incomplete information, elevating both regulatory and development risk.

The framework defines comparability as an ongoing, life cycle–based risk management obligation rather than a single regulatory milestone. Each process change becomes a decision point requiring structured evaluation of potential impact on product quality and performance, supported by data that are proportionate to the level of risk introduced.

Potency occupies a central role in this risk-based view of comparability. The FDA requires potency testing to help assure key attributes of CGT products, including identity, purity, strength, and stability, across all phases of clinical development and after approval. These tests are not simply release criteria; they are critical tools that ensure that only lots that meet defined specifications and acceptance criteria are administered to patients.⁸

Because no single assay is likely to capture the full functional profile of a complex CGT product, the FDA recognizes that multiple potency assays may be necessary. This concept, often described as an assay matrix, reflects the need to combine complementary analytical and functional measurements to build confidence that product performance remains consistent following manufacturing changes.⁷

Acceptance criteria for these assays are expected to play a direct role in risk reduction. The FDA emphasizes that potency assays and their corresponding limits should be designed to make meaningful contributions to potency assurance by reducing the risk that manufacturing variability translates into clinically meaningful differences. In this way, analytical complexity is not incidental but foundational to the comparability strategy, linking manufacturing control to clinical reliability through a structured, risk-based framework.

These regulatory case examples illustrate how comparability is evaluated in practice for different CGT modalities and how manufacturing changes intersect directly with questions of product identity, clinical relevance, and regulatory acceptability.

In its assessment of Casgevy, a genome-editing therapy, the EMA placed explicit emphasis on the sponsor’s comparability strategy for manufacturing site transfer and for newly synthesized batches of single guide RNA (sgRNA). Regulatory scrutiny extended beyond high-level process descriptions to detailed consideration of analytical testing designed to support product performance continuity following these changes. The agency evaluated how the sponsor addressed potential differences introduced through site transfer and material changes by examining analytical comparability across multiple dimensions, including potency assessment, off-target analysis, drug product release criteria, and the suitability of the stability program.⁹

This case demonstrates that, for genome-editing therapies, comparability is inseparable from molecular control. Manufacturing changes that alter critical inputs or production locations trigger expectations for expanded analytical justification, particularly where such changes could affect genome targeting or functional activity. The Casgevy review reflects a regulatory view that comparability strategies must be explicitly planned and documented when development programs transition between sites or material sources.

The EMA assessment of Carvykti, a chimeric antigen receptor T (CAR-T) cell therapy, highlights the difficulty of establishing comparability between clinical and commercial manufacturing processes for cell-based products. In its public assessment report, the agency concluded that comparability of commercial product with clinical trial lots could not be fully established at the quality level. This finding underscores the challenge of demonstrating equivalence when manufacturing processes evolve late in development and when biological variability remains high.¹⁰

The agency further noted that only a limited number of patients had been treated with material produced using the commercial process. While available data supported efficacy, the small data set meant that slight differences between clinical and commercial lots could not be excluded. This regulatory posture illustrates the evidentiary tension that can arise when scale-up or process changes occur close to approval: even when clinical performance appears consistent, uncertainty at the quality level can persist due to limited exposure and incomplete comparability data.

For Hemgenix, an adeno-associated virus (AAV) gene therapy, the EMA’s evaluation process formally incorporated comparability planning into scientific advice and protocol assistance discussions. The agency recommended that the sponsor seek guidance on an overall comparability strategy to support anticipated changes in manufacturing and formulation. This recommendation was made early enough in development to frame comparability as a forward-looking design consideration rather than a retrospective justification exercise.¹¹

The Hemgenix assessment further specified that the comparability strategy needed to address both phase III clinical material and commercial-scale vector production. By linking comparability expectations across late-stage development and commercialization, the agency signaled that manufacturing continuity must be demonstrated not only within a single development phase but across the full transition from clinical to commercial supply. This case exemplifies how regulators view comparability for vector-based gene therapies as a life cycle obligation that spans site changes, scale-up, and process maturation.

The FDA provides formal regulatory mechanisms to help sponsors manage manufacturing changes in a structured and predictable way, most notably through the use of comparability protocols. These protocols allow sponsors to predefine the specific tests, validation studies, and acceptance limits that will be used to demonstrate that a proposed manufacturing change does not adversely affect product quality or performance. Rather than treating each change as an ad hoc regulatory event, a comparability protocol establishes an agreed-upon framework for how evidence will be generated and evaluated when changes occur.^2,12,13

Once reviewed and accepted, comparability protocols can be incorporated into an original application or submitted after approval and used as a standing strategy for managing future changes. Importantly, the FDA notes that a single protocol may apply either to one-time changes or to a defined category of changes that recur over the product’s life cycle. This approach reflects an expectation that manufacturing evolution is inevitable, particularly for CGT products, and that regulatory oversight can be made more efficient when sponsors anticipate and systematize how comparability will be demonstrated over time.¹³

In this sense, comparability protocols function as both technical and strategic tools. They shift the focus from reactive justification of individual changes to proactive life cycle planning, embedding comparability into development and commercialization pathways rather than treating it as an episodic regulatory hurdle.

Life cycle management of comparability is grounded in the core requirements of investigational and commercial regulatory submissions. For IND applications, the FDA requires sponsors to provide information describing the composition, manufacture, and control of the drug substance and drug product. This foundational expectation establishes manufacturing transparency as a prerequisite for clinical investigation and creates the baseline against which subsequent changes must be evaluated.¹⁴

These expectations extend into chemistry, manufacturing, and controls (CMC) requirements, which must assure critical product attributes including identity, strength, quality, purity, and stability. For CGT products, these attributes are not abstract quality descriptors but integral components of clinical reliability, linking manufacturing consistency directly to patient exposure and therapeutic effect. As a result, comparability across the product life cycle becomes inseparable from the obligation to maintain robust CMC systems capable of detecting and controlling change.^14,15

Together, IND and CMC requirements reinforce the concept that comparability is not confined to a single development milestone. Instead, it is embedded within the regulatory architecture governing how products are made, characterized, and justified from first-in-human studies through commercial production. Managing comparability across the life cycle therefore depends not only on analytical data but on sustained alignment between manufacturing strategy and regulatory expectations.

For contract development and manufacturing organizations (CDMOs), comparability is not an abstract regulatory concept but a central operational risk. Regulatory guidance makes clear that manufacturing changes without adequate comparability data can trigger clinical holds and that this risk applies at any stage of development if safety or effectiveness may be affected.^2,3 Because CDMOs frequently support multiple process iterations across development phases, they operate at the intersection of technical execution and regulatory consequence. In this environment, change control functions as a form of regulatory risk management, not simply as a quality system requirement.

The stakes increase sharply as products advance into late-stage clinical development. Both the FDA and EMA highlight that manufacturing changes introduced closer to pivotal trials or commercialization are the most challenging to justify, owing to the growing dependence on accumulated clinical data and the reduced tolerance for uncertainty. Substantial process modifications during pivotal studies are discouraged, and late-stage changes demand more extensive evidence to demonstrate that product performance remains unaffected. For CDMOs, this means that decisions about facility transfers, scale-up, or process optimization must be evaluated not only for technical feasibility but also for their potential impact on the sponsor’s regulatory trajectory.

Regulatory case experience further reinforces that comparability strategies are expected to span the full transition from clinical development to commercial manufacturing. In the Hemgenix assessment, EMA explicitly required a comparability strategy that addressed both phase III material and commercial-scale vector production, signaling that continuity of manufacturing control across stages is a regulatory expectation rather than an optional refinement. This life cycle perspective places CDMOs in a strategic role: their platforms, analytical capabilities, and change management practices become integral to the sponsor’s ability to demonstrate product consistency over time.

These dynamics elevate the importance of platform-based analytics and potency strategies within CDMO operations. Because CGT products often require multiple complementary assays to characterize functional attributes, CDMOs must be prepared to support assay matrices and acceptance criteria that meaningfully reduce risk to product potency. Early establishment of these analytical frameworks can make later comparability exercises more defensible and less disruptive, particularly when programs approach pivotal trials or commercial readiness.

The regulatory landscape suggests that CDMOs are no longer simply executing predefined processes; they are actively shaping the comparability narrative for CGT products. Early planning for manufacturing evolution, disciplined change control, and investment in robust analytical platforms position CDMOs to support sponsors through the most vulnerable phases of development. In this context, comparability is not a downstream regulatory hurdle but a core design principle for CGT manufacturing partnerships, influencing decisions from process development through commercial scale.

Across regulatory guidance and real-world assessments, a consistent picture emerges: comparability for CGT products is inherently more fragile than for conventional biologics. The combination of biological variability, complex functional attributes, and limited manufacturing experience makes it more difficult to demonstrate that a post-change product is truly equivalent to its pre-change predecessor. For cell- and tissue-based therapies in particular, regulators recognize that traditional comparability frameworks are strained by the scientific and statistical limits of characterizing living systems.

Regulatory tolerance for uncertainty narrows as development advances. Flexibility that may be acceptable in preclinical or early clinical stages progressively diminishes as programs enter pivotal trials, where accumulated clinical data become the foundation for approval decisions. At that point, manufacturing changes are no longer viewed as routine refinements but as potential threats to the interpretability and credibility of the clinical evidence base.

The case examples reinforce this principle in practical terms. Reviews of Casgevy, Carvykti, and Hemgenix show that regulators closely scrutinize comparability when products undergo manufacturing site transfers, material changes, or transitions from clinical to commercial scale. Expectations extend beyond high-level process descriptions to detailed analytical strategies encompassing potency, release criteria, stability, and, where relevant, molecular specificity. These examples demonstrate that comparability is not a theoretical construct but a decisive factor in regulatory confidence during scale-up and technology transfer.

These trends support a central conclusion: in CGT, manufacturing strategy and regulatory success are inseparable. Because process changes can alter product identity in ways that are difficult to predict or reverse, comparability must be treated as a core design principle rather than a downstream justification exercise. For sponsors and CDMOs alike, this means that decisions about process development, analytical frameworks, and site transitions are simultaneously scientific, operational, and regulatory decisions. In this sense, the long-standing maxim that “process equals product” is not merely preserved in CGT — it is magnified.

1. Comparability of Biotechnological/Biological Products Subject to Changes in their Manufacturing Process Q5E. International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use. 18 Nov. 2004.

2. Manufacturing Changes and Comparability for Human Cellular and Gene Therapy Products: Draft Guidance for Industry. U.S. Department of Health and Human Services. Jul 2023.

3. CFR 21 312.42 Clinical holds and requests for modification. Code of Federal Regulations. 24 Mar. 2004.

4. “IND Application Procedures: Clinical Hold.” U.S. Food and Drug Administration. Accessed 26 Jan. 2026.

5. “Questions and answers: Comparability considerations for Advanced Therapy Medicinal Products (ATMP).” European Medicines Agency. 6 Dec. 2019.

6. Human Gene Therapy Products Incorporating Human Genome Editing: Guidance for Industry. U.S. Department of Health and Human Services. Jan. 2024.

7. Potency Assurance for Cellular and Gene Therapy Products: Draft Guidance for Industry. U.S. Department of Health and Human Services. Dec. 2023.

8. Potency Tests for Cellular and Gene Therapy Products: Guidance for Industry. U.S. Department of Health and Human Services. Jan. 2011.

9. Assessment report: Casgevy. European Medicines Agency. 14 Dec. 2023.

10. Assessment report: Carvykti. European Medicines Agency. 24 Mar. 2022.

11. Assessment report: Hemgenix. European Medicines Agency. 15 Dec. 2022.

12. CFR 21 601.12 Changes to an approved application. Code of Federal Regulations. Accessed 26 Jan. 2026.

13. Comparability Protocols for Human Drugs and Biologics: Chemistry, Manufacturing, and Controls Information: Guidance for Industry. U.S. Department of Health and Human Services. Apr. 2016.

14. CFR 21 312.23 IND content and format. Code of Federal Regulations. 24 Mar. 2004.

15. Chemistry, Manufacturing, and Control (CMC) Information for Human Gene Therapy Investigational New Drug Applications (INDs): Guidance for Industry. U.S. Department of Health and Human Services. Jan. 2020.