Cepheid and Oxford Nanopore Technologies Partner on Advancing Automated Sequencing-Based Solutions

By LabMedica International staff writers
Posted on 10 Apr 2025

$Image: The collaboration aims to leverage Oxford Nanopore\'s sequencing platform and Cepheid\'s GeneXpert system to advance the field of sequencing for infectious diseases (Photo courtesy of Cepheid)$

Image: The collaboration aims to leverage Oxford Nanopore\'s sequencing platform and Cepheid\'s GeneXpert system to advance the field of sequencing for infectious diseases (Photo courtesy of Cepheid)

Cepheid (Sunnyvale, CA, USA), a leading molecular diagnostics company, and Oxford Nanopore Technologies (Oxford, UK), the company behind a new generation of sequencing-based molecular analysis technologies, have entered into a strategic collaboration to develop and commercialize a seamless end-to-end workflow that combines Cepheid's GeneXpert system for pre-sequencing sample and library preparation with Oxford Nanopore's rapid, information-rich molecular analysis platform.

The two companies have completed a successful proof-of-concept study which demonstrated the feasibility of using Cepheid's cartridge-based GeneXpert system for sample and library preparation in a workflow with Oxford Nanopore's sequencing platform. The positive results from the proof-of-concept have paved the way for the strategic collaboration to develop and launch a joint Research Use Only (RUO) workflow that will enable customers to leverage rapid, information-rich sequencing in-house for infectious disease analysis, returning results within hours instead of days. The initial application of the workflow will focus on infectious disease, specifically the profiling of bacterial and fungal pathogens with whole genome sequencing first from culture isolates and eventually directly from positive blood cultures. The collaboration has the potential to expand from this initial application into additional infectious disease use cases, other areas such as cancer and human genetics, and eventually regulatory approved clinical diagnostics.

The collaboration is intended to deliver a scalable, automated, end-to-end solution for simplified nanopore sequencing workflows for use within a range of settings, including labs that have previously not had the expertise to conduct sequencing in-house. The joint workflow will be compatible with a range of third-party informatics tools including Oxford Nanopore's EPI2ME, and other informatic solutions that are part of Oxford Nanopore's compatible provider network. Cepheid will also complement the joint workflow by directly offering an informatics solution, which they will commercialize by way of a license from a leading industry player; this informatics platform provides comprehensive pathogen identification, comprehensive antimicrobial resistance gene detection, SNP-based clonality for outbreak tracking and surveillance, and AI-driven genotypic antimicrobial susceptibility predictions.

"Combining the ease-of-use of the GeneXpert system, the most widely placed PCR diagnostic instrument world-wide, with Oxford Nanopore's unique sequencing platform, unlocks a richness of biomarker data that has historically been technically challenging for many labs to access," said Vitor Rocha, President of Cepheid. "Providing an integrated solution to more effectively characterize infectious diseases, understand the epidemiology of bacterial outbreaks, and profile antimicrobial resistance will meaningfully accelerate our mission of expanding access to critical molecular information. The potential for future expansion of this technology to applications for patient care is exciting."

"This collaboration represents an important step forward in delivering new and improved workflow options to better understand infectious diseases," added Dr. Gordon Sanghera, CEO of Oxford Nanopore Technologies. "By partnering to integrate our richer data, rapid insights, and accessible and affordable sequencing technology with Cepheid's GeneXpert architecture, we are establishing a workflow foundation that is positioned for future expansion into scaled routine clinical use."