Oxford Nanopore Biopharma Day

RNA-based medicines have the potential to transform the prevention and treatment of a wide range of diseases. However, achieving clinical success depends on overcoming a major hurdle: actionable quality control. Traditional analytical methods often fall short in providing the resolution needed to fully characterize RNA critical quality attributes (CQAs) that impact therapeutic efficacy and safety.

Eclipsebio’s eMERGE platform addresses this need by applying sequencing-based technologies to reveal key insights into the quality and behavior of RNA therapeutics. Through comprehensive, high-resolution analyses, eMERGE directly measures essential CQAs, including RNA secondary structure within lipid nanoparticles (LNPs), the presence of fragmented or degraded RNA species, and poly(A) tail length variability.

In this presentation, we will highlight how eMERGE, powered by Oxford Nanopore sequencing, supports the development and manufacturing of RNA-based therapies by delivering detailed, actionable data across multiple dimensions of RNA quality. By integrating these advanced assessments into development workflows, therapeutic programs can better ensure product consistency, reduce risk, and accelerate progress toward clinical success.

Affinity maturation and related antibody engineering usually requires variant libraries of a parental sequence. For scFv libraries, phased mutations are lost if sequencing using short-read technologies, whereas previous sequencing error rates have limited the use of long-read sequencing. With the advent of UMI longread sequencing, rapid medium-throughput sequencing of libraries can be achieved, which enables deeper analysis of library variants.

Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by the loss of dopamine-producing neurons in the substantia nigra, resulting in significant motor impairment. While current therapies offer symptomatic relief, they do not halt disease progression. At Aspen Neuroscience, we are developing a personalized, autologous neuron replacement therapy by using patient-derived induced pluripotent stem cells (iPSCs) differentiated into dopamine neuron precursors for transplantation. In this autologous approach, ensuring genomic integrity and safety of each patient-specific cell product is of utmost importance. To address this need, we are evaluating the integration of Oxford Nanopore Technologies (ONT) long-read sequencing in-house. ONT enables real-time, long read WGS with methylation profiling in a single assay. Initial validation shows enhanced detection of structural variants, improved workflow efficiency and faster turnaround times, while maintaining control over sensitive genomic data. I will present our transition from outsourced short-read sequencing to internal ONT-based workflows, ongoing benchmarking against Illumina-based results and implications for our future manufacturing and QC strategies. By adopting long-read sequencing technologies we aim to deliver safer, more precise and personalized neural cell therapies for patients with PD.

The Pfenex Expression Technology® (Pfenex) is a clinically and commercially validated therapeutic protein expression platform using Pseudomonas fluorescens as a production host. Pfenex benefits include an extensive toolbox of expression vectors, modified host strains, and additional genetic elements that when combined with an automated, high throughput combinatorial screening efficiently generates production strains for high protein titer and quality challenging proteins. The base Pfenex workflow requires screening and analysis of thousands of unique expression strains with different toolbox combinations within ~10-12 weeks. A newly developed platform, Pfast™, provides actionable insights on protein expression in just 10 days through a pooled cloning strategy. Here we show how the Oxford Nanopore long-read sequencing technology enables evaluation of these pools to deconvolute the pooled constructs into individual clones for continued optimization. The versatility of the Oxford Nanopore platform has contributed significantly to increased throughput, improved accuracy, and lower costs that benefit early drug development.

Recombinant adeno-associated virus (rAAV) vectors are a leading platform for gene therapy, with growing demand for engineered capsids that offer improved targeting and reduced toxicity. As clinical pipelines expand, robust analytical tools are essential to accurately characterize viral genomes and detect residual DNA species in vector products.

We present a dual-platform sequencing strategy that integrates both short read and Oxford Nanopore long read technologies to evaluate rAAV vectors with a focus on packaging efficiency and genome integrity. This approach enables detailed analysis of ITR structures, terminal hotspots, size distribution, structural variants, and residual content—factors critical to vector potency, purity, and safety. Results are compared against standard analytical techniques such as PCR, gel electrophoresis, and analytical ultracentrifugation (AUC). Our workflow enhances sequence resolution, supports precise quantification, and streamlines quality assessment in both process development and manufacturing