Franklin Biolabs CEO Selected as a 2026 Women of Influence by the Philadelphia Business Journal
Learn more

Custom NGS Assay Development for RNA Therapeutics and LNP Delivery

PROVEN INTELLIGENCE IN RNA THERAPEUTIC ANALYTICS.

Custom NGS Assay Development for RNA Therapeutics and LNP Delivery

CELL & GENE | RNA | BIOLOGICS

A stylized rendering of a DNA double helix on the left side of a light blue gradient background.

Executive Summary

For sponsors developing RNA therapeutics delivered via lipid nanoparticle (LNP) systems, standard analytical methods often fail to provide the necessary resolution to fully characterize the asset. Custom Next-Generation Sequencing (NGS) assays offer a definitive solution for quantifying payload integrity, non-target tissue biodistribution, and in vivo stability. This approach moves beyond simple titer measurements to provide a comprehensive data package that de-risks development, satisfies global regulatory expectations, and accelerates timelines toward IND submission.

Frequently Asked Questions

Why are custom NGS assays necessary for LNP and RNA therapeutic programs?

Standard analytical tools like qPCR can quantify payload presence but may not adequately assess its integrity, sequence fidelity, or potential truncations post-administration. Custom NGS assays provide deep sequence coverage, enabling precise characterization of the RNA payload within biological samples and offering a more complete picture of product quality and in vivo behavior for IND-enabling toxicology studies.

How does advanced analytical characterization impact the timeline for an Investigational Medicinal Product Dossier (IMPD)?

A robust analytical data package is foundational to a successful IMPD or IND submission. By developing and qualifying custom NGS assays early, sponsors can proactively address regulatory questions on product consistency, purity, and stability. This minimizes delays and aligns with the 18-24 month IND timelines our scientific leadership has consistently achieved.

Can these NGS assays be developed and run under GxP conditions?

Yes. All custom assays are developed and qualified in a phase-appropriate manner. For pivotal IND-enabling studies, assays are validated to meet GxP compliance standards, ensuring the data is reliable, reproducible, and suitable for submission to global regulatory bodies like the FDA and MHRA.

The analytical strategy for RNA therapeutics and their LNP delivery systems requires a level of precision that exceeds the capabilities of many legacy platforms. The dynamic nature of RNA payloads and their interaction with LNP components demand methods that provide a comprehensive assessment of quantity, quality, and sequence fidelity from the drug product to the biological matrix.

Franklin Biolabs develops custom NGS-based analytical solutions specifically for these next-generation therapeutics. Our approach provides a multi-attribute characterization of the therapeutic candidate, which is a requirement for building a data package that withstands regulatory scrutiny.

Comprehensive Characterization Beyond Titer

A complete understanding of an RNA therapeutic’s in vivo performance depends on answering several key questions:

  • Payload Integrity: Is the full-length, correct RNA sequence present in the target tissue?

  • Biodistribution: What is the precise quantification of the therapeutic in both target and non-target tissues?

  • Stability: How does the RNA payload persist and behave within different biological compartments over time?

Custom NGS assays directly address these points by enabling deep sequencing of RNA recovered from biological samples. This provides definitive data on sequence variants, truncations, and modifications, which is information that can be missed by other methods.

A close-up, blue-toned image of scientific glassware, featuring vials placed in a dish filled with clear, spherical beads, suggesting a laboratory or research setting.

Accelerating Candidate Selection with High-Throughput Screening

The strategic value of NGS extends into early-phase development. As demonstrated in foundational research on LNP delivery, high-throughput sequencing of barcoded mRNA payloads allows for pooled in vivo administration and simultaneous quantification across multiple organs (PMID: 31678653). The translational impact of this methodology is significant: it accelerates the identification of lead LNP candidates and optimal formulation parameters, directly reducing the time and resources required for preclinical screening.

This level of analytical intelligence is integrated into our programs, supported by our >100,000 sq ft of specialized laboratory and preclinical housing space.

Our scientific team’s track record, which includes a 100% successful IND rate since 2019, was established on this principle of using superior analytical methods to build robust, defensible data packages. While Franklin Biolabs was formally launched in 2024, this success rate reflects the deep history of our core scientific leadership and principal scientists in navigating complex programs, including our work supporting Moderna’s RNA platform. For more information on our broader analytical capabilities, please see our core Vector | CMC | Analytics Services page.

Scientific Process Diagram

This content is for informational purposes. For guidance specific to your therapeutic program, please contact our team for a consultation.

Explore More Capabilities