Oxford Nanopore and PathoQuest announce next step of strategic collaboration to bring to market the first sequencing-based quality control test for biopharma genetic characterisation

Nanopore sequencing combined with PathoQuest expertise offers a new approach for biologics manufacturing with real-time, accurate testing for genetic characterisation, cutting months off traditional methods and providing more complete data.

Oxford Nanopore Technologies plc (Oxford Nanopore) and PathoQuest SAS today announce the signing of a definitive agreement to co-develop a transformational Integration Site Analysis (ISA) test to provide a Good Manufacturing Practice (GMP) validated nanopore sequencing-based commercial testing service to the biopharma industry. This is designed to address the needs of industrial developers and manufacturers of biological products, for example monoclonal antibodies or novel proteins that may be used across the life sciences/healthcare industry.

Oxford Nanopore’s technology can read any length of native DNA with high accuracy, meaning that the technology can identify and comprehensively sequence gene insertion sites without the risk of missing off target integrations. In addition, the PathoQuest ISA test will leverage real-time data streaming, enabling rapid and accurate clone identification, with the potential to speed up biopharma manufacturing Quality Control (QC) testing by months over traditional methods and therefore to support faster or more effective outcomes for biopharma.

Biologics manufacturing

Most biologics (including monoclonal antibodies (mAbs) and recombinant proteins) are manufactured using genetically modified cell lines. For many cell therapies, the product itself is a genetically modified cell line. Throughout the development of these products, it’s important to characterise and monitor the genetic modification(s) that have been made and assure the quality and safety of the product. Classical tests for this application have limitations in terms of scalability, speed and the completeness of data provided.

This brand-new test will allow sequencing of both the transgene and the genomic insertion site, overcoming the limitations of existing methodologies and delivering an accurate and rapid QC test for modified cell lines.

Oxford Nanopore and PathoQuest intend the ISA test to be the first in a line of sequencing-based QC test solutions targeting the biopharma genetic characterisation and safety market.

Genetic characterisation for monoclonal antibodies

mAbs and their derivatives are transformative drugs that have enabled the treatment of complex indications in oncology, immunology and other therapeutic areas. There are now more than 170 mAbs and antibody derivatives designated as drugs with new approvals increasing yearly.

To develop a manufacturing cell line for mAbs, antibody encoding genes (transgenes) need to be stably integrated into mammalian cells, generally Chinese Hamster Ovary (CHO) cells, to develop both Master and Working Cell Banks for future commercial manufacturing batches. However, the identification of a CHO cell line which produces high amounts of the mAb is extremely challenging and resource intensive using current gold standard methods.

To make situations more complex, the transgene encoding for the antibody may not always integrate correctly and can be truncated, rearranged, duplicated and/or integrate in unwanted locations. With classical methods, identifying an optimal cell line clone requires screening using a multitude of different tests to detect stable and correct integration sites before the mAb’s desired mode of action can be explored and a high producing cell can be identified.

Current gold standard methods for the characterisation of the mAb cell banks are slow and error prone, with random off target integrations potentially missed. Long nanopore reads allow for sequencing the vector and the transgene – as opposed to only focusing on the transgene with short-reads – giving a broader picture on what has been developed and a stronger guarantee of accuracy, expediting the development process.

The PathoQuest validated ISA test will allow for rapid initial clone selection and subsequently will provide assurance that the desired high production mAb cell bank is maintained throughout the entire development and manufacturing life cycle, thus significantly reducing production risks.

Genetic characterisation for cell therapy

Cell therapy is a rapidly growing field. Pharmaceutical companies have invested significantly in this area and an increasing number of products are now licensed in regenerative medicine, immune diseases, and cancer.

ISA is also important in cell therapy, where genetically modified cells are often the product itself. A comprehensive and thorough understanding of the integration locations and frequency is important to ensure the safety and quality of these products.

Gordon Sanghera, CEO, Oxford Nanopore Technologies, commented:

“We are pleased to announce the next step of our partnership with PathoQuest, and we are excited to start on the development of this breakthrough test for biologics manufacturing. Nanopore sequencing offers a transformational new approach for robust and accurate genetic characterisation of biological materials, which we believe will enable the release of novel therapeutics with more certainty and safety assurance than ever before.

Jean-François Brepson, CEO, PathoQuest commented:

“We are excited to be selected as the partner of choice in biologics Quality Control services by Oxford Nanopore Technologies. We will use our know how and expertise to optimise and validate this Integration Site Analysis test, bringing it to market as a GMP service from our facilities in Paris France and Wayne PA. It will enable our customers to understand their cell lines more comprehensively and more quickly so they can proceed with more certainty.”