Nanopore sequencing in biopharma research and development: transforming precision medicine and antibody discovery
By Heather Stark, Biopharma Market Segment Manager, Oxford Nanopore Technologies.
As biopharma research and development (R&D) continues to evolve, the demand for innovative tools that accelerate discovery is greater than ever. Oxford Nanopore is leading this transformation, addressing key challenges in biomarker discovery, antibody production, and quality control.
This blog explores how nanopore sequencing is reshaping biopharma R&D and driving innovation in precision medicine.
Transforming biomarker discovery
Identifying genetic and epigenetic variants is an essential step in the discovery of novel biomarkers, because these variants often drive the biological processes that distinguish healthy cells from disease states.
Nanopore sequencing is transforming biomarker discovery by offering an unmatched combination of resolution and flexibility across its sequencing platform.
While traditional technologies struggle to capture the vast complexity of genetic and epigenetic variants, Oxford Nanopore’s DNA and RNA sequencing technology is capable of directly sequencing reads of any length. This flexibility enables more effective and comprehensive biomarker identification.
Wasatch BioLabs, for example, have utilised nanopore sequencing to develop a novel cfDNA methylation assay called NESSI-Seq, which provides higher resolution and more comprehensive CpG coverage than alternative existing methods. Methylation in key promoter genes or CpG’s can influence therapeutic protein expression, and this evolution paves the way for new applications in oncology and neurodegenerative diseases.
“Nanopore technology offers unprecedented resolution and coverage, revolutionising our approach to biomarker discovery,”’
Chad Pollard from Wasatch Labs.
Arena Bioworks is also using nanopore sequencing to develop advanced structural variant (SV) assays, crucial for detecting complex genetic rearrangements like ROS1 and ALK fusions in cancer. These SV assays are pivotal for clinical trial eligibility and personalised treatments. “Oxford Nanopore sequencing could be a one-stop shop for complex cases like cancer fusion detection, overcoming limitations in base accuracy and offering cost-effective solutions,” says Dr Tasos Gogakos, from Arena Bioworks.
Advancing antibody discovery through multiomics
Nanopore sequencing is also advancing antibody discovery through its multiomics approach, combining genomic, transcriptomic, and epigenomic data to provide unprecedented insights into immune responses.
Scott Hickey, Director of Genomic Applications at Oxford Nanopore, demonstrated how nanopore sequencing is being used for de novo monoclonal antibody discovery, analysing single-cell transcriptomes and the haplotype-resolved germline of the Ig locus. This comprehensive approach ensures detection of even rare antibodies, offering a complete picture of immune responses.
“Nanopore sequencing offers unparalleled read lengths, allowing us to capture the full complexity of antibody genes and their diverse isoforms,”
Scott Hickey, Director of Genomic Applications, Oxford nanopore Technologies
These insights are crucial for developing novel antibodies that can target infectious diseases, further establishing nanopore sequencing as a pivotal tool in antibody research.
Enhancing antibody production with precision genome engineering
Nanopore sequencing is further playing a critical role in improving antibody production in Chinese Hamster Ovary (CHO) cells, widely used in biopharmaceutical manufacturing. By integrating nanopore multiomics data, biopharma companies are optimising CHO cell lines to boost both yield and quality.
Lonza and Sanofi are both leveraging nanopore sequencing to map gene editing success in CHO cells to identify any on or off targets effects, enhancing productivity through an improved detection of genomic variants. “The internal reference genomes improve omics analysis accuracy, leading to better research and production methodologies,” says Daniel K. Fabian from Lonza.
Integrating DNA methylation data has further revealed new insights into gene expression, allowing researchers to identify top-producing antibody clones and streamline production processes.
A future of precision and innovation
As biopharma R&D progresses, the demand for accurate, scalable genomic tools continues to grow. Oxford Nanopore Technologies is meeting this need, enabling biomarker discovery, antibody research, and enhanced CHO cell productivity. As more companies adopt nanopore sequencing, the future of drug discovery and development promises even greater precision and innovation.