Oxford Nanopore Biopharma Day

DNA sequencing is an essential step in many Pfizer-BMD workflows, from identifying screening hits to verifying plasmid sequences for the development of stable cell lines and finally sequencing the completed cell line. Traditionally, most sequencing was outsourced to external vendors using Sanger Sequencing, which was slow, costly, and unable to resolve potential mixed populations. Since early 2023, we have adopted in-house Oxford Nanopore sequencing as the primary method in BMD. Our new sequencing pipeline is more reliable, significantly faster, cheaper, and provides deeper insights by resolving mixed populations and enabling rapid sequencing of full plasmids.

We present a next-generation analytical strategy for mRNA vaccines and therapeutics that leverages Long-read Direct RNA sequencing to consolidate multiple critical quality attributes (CQAs) into a single sequencing assay. Direct RNA sequencing on a GridION Q-Line provides full-length, primer-agnostic reads to assess identity across the open reading frame and quantify polyA tail length distributions. Long reads resolve multivalent products by aligning to component-specific references, enabling accurate and reproducible mass-ratio measurements and eliminating co-elution ambiguities seen with conventional RP-IP HPLC. In parallel, plasmid sequencing with an internally developed polishing algorithm improves raw read accuracy to >99.9%, enabling highly sensitive automatic variant calling, and rapid barcoding of circular plasmids supports polyA tail estimation. Collectively, these capabilities address the shortcomings of Sanger and short-read NGS for multivalent, sequence-similar constructs and reduce method burden by unifying CQA measurements from a single library preparation. We outline an aspirational path toward a streamlined, multi-attribute release test for mRNA drug products and complementary plasmid testing, advancing both development decisions and release methods.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.

To follow

We will showcase the genomics services offered by GENEWIZ, uniquely powered by Oxford Nanopore Technologies, to deliver comprehensive solutions for a wide range of research applications. Featured services include rapid whole plasmid and amplicon sequencing, direct RNA sequencing to capture native transcriptomes and RNA modifications, ultra-long DNA sequencing for resolving complex genomic regions, and adaptive sampling to enrich target regions without the need for time-consuming or costly probe or primer design. These capabilities enable fast, flexible workflows tailored to the evolving needs of biopharma research.