To listen to the podcast version of the article, click here.

Biomarker Assay Validation: Why a Paradigm Shift Was Long Overdue

Introduction: A New FDA Guideline—But Are We Still Thinking in Old Frameworks?

In January 2025, the U.S. Food and Drug Administration (FDA) released its long-awaited guidance on Bioanalytical Method Validation for Biomarkers (BMVB). This document replaces the 2018 guidance and marks a significant regulatory milestone: the formal separation of biomarker assay validation from pharmacokinetic (PK) assay validation.

But what does this shift mean in practice? And why is biomarker assay validation fundamentally different?

Ask the Scientists

Context Is King: Why “Fit-for-Purpose” Is More Than a Buzzword

The FDA’s new guidance emphasizes a fit-for-purpose (FFP) approach. In simple terms, this means that assay validation must be tailored to the Context of Use (COU)—the specific role a biomarker plays in drug development.

Unlike PK assays, which serve a singular purpose (measuring drug concentrations), biomarker assays support a wide range of applications:

Understanding mechanisms of action (MoA)
Patient stratification and selection
Assessing pharmacodynamic effects
Evaluating safety signals
Supporting proof-of-concept in early-phase trials

This diversity makes it impractical—and potentially misleading—to apply the rigid framework of ICH M10, which was designed for PK assays, to biomarker assays.

Ask the Scientists

The Challenge: No Universal Reference Standard

One of the most critical differences lies in the availability of reference materials. PK assays typically use the drug product itself as a fully characterized standard. Biomarker assays, however, often rely on synthetic or recombinant proteins that differ from the endogenous analyte in key ways—such as folding, glycosylation, or truncation.

This leads to several implications:

Spike-recovery tests may not reflect actual assay performance for the endogenous biomarker.
Relative accuracy replaces absolute accuracy.
Parallelism becomes essential to demonstrate comparability between calibrators and native analytes.

Biological Variability: The Hidden Complexity

Biomarker data is influenced not only by analytical performance but also by biological variability—differences between individuals in expression levels, matrix composition, and physiological conditions. This variability must be accounted for during assay development and data interpretation, adding another layer of complexity to validation strategies.

Ask the Scientists

Regulatory Clarity: What the FDA Actually Says

The 2025 BMVB guidance does not introduce new analytical requirements. Instead, it clarifies that biomarker assay validation must be scientifically justified and context-specific. Sponsors are expected to include rationale and justification for deviations from PK validation protocols in their method validation reports.

Ask the Scientists

Recommended Actions for Sponsors

The article’s authors suggest several best practices:

Include a COU statement in every biomarker assay validation report.
Engage with regulatory agencies early, especially when biomarker data will influence approval decisions or when novel technologies are involved.
Avoid using the term “qualification” for biomarker assays. The FDA defines qualification only in the context of biomarkers—not assays. Instead, use “validation” or “fit-for-purpose validation” to avoid regulatory confusion.

Conclusion: Science Over Standardization

Biomarker assay validation is not a technical footnote—it’s a strategic pillar in modern drug development. Applying PK-centric validation frameworks to biomarker assays risks generating misleading data and regulatory setbacks.

The FDA’s new guidance sends a clear message: contextualization, scientific rigor, and methodological flexibility are the new standards. Biomarker assays must be validated not by rigid templates, but by thoughtful, purpose-driven approaches that reflect their biological and clinical complexity.

Frequently Asked Questions (FAQ)

What’s the difference between PK and biomarker assays? PK assays measure drug concentrations. Biomarker assays detect biological signals that inform various aspects of drug development.

Why doesn’t ICH M10 apply to biomarker assays? ICH M10 assumes the availability of a fully characterized reference standard, which is often not feasible for biomarkers.

What does “fit-for-purpose” mean in assay validation? It means tailoring the validation strategy to the biomarker’s intended use in drug development.

Do I need new validation procedures for biomarkers? Not necessarily. But you must justify any deviations from PK validation protocols and align your strategy with the biomarker’s COU.

This article is based on and critically reflects the findings and interpretations presented in:

Ni, Y. G., Stevenson, L. F., Neely, R. J., Amaravadi, L., Fernández-Metzler, C., King, L., Piccoli, S. P., Hays, A., Gorityala, S., Ghosh, D., Bean, S. M., Cape, S., Dalmasso, E. A., Green, J., Gunsior, M., Hassanein, M., Laxmanan, S., Pandey, A., Qiu, X., Tinder, C., Zeng, J., Zoghbi, J., Quadrini, K. J., & the AAPS Biomarkers and Precision Medicine Community Leadership Team. (2025). Why is biomarker assay validation different from that of pharmacokinetic assays? AAPS Journal, 27, Article 147. https://doi.org/10.1208/s12248-025-01135-5

Ask the Scientists