Oxford Nanopore Technologies and Saphetor announce a new partnership to deliver tertiary analysis for comprehensive interpretation of nanopore sequencing

This new partnership will provide integrated end-to-end solutions from sample to report for whole genome nanopore sequencing in future clinical applications.

Oxford Nanopore Technologies plc (Oxford Nanopore), the company delivering a new generation of nanopore-based molecular sensing technology, and Saphetor, the next generation sequencing data analysis company, today announce a new partnership to support the comprehensive analysis of nanopore sequencing data and to enable end-to-end workflows.

The collaboration with Saphetor will enable a direct connection between secondary and tertiary analysis, connecting Oxford Nanopore EPI2ME™ research software with VarSome Clinical, a CE-marked IVD medical device and HIPAA-compliant platform from Saphetor. This will deliver an integrated solution from sample to variant interpretation.

Oxford Nanopore’s sequencing platform currently offers research tools to make sense of raw sequencing signal and offer initial analysis, including basecalling. Primary tools use AI to transform the raw signal into sequencing data through device software, MinKNOW™. Secondary analysis focuses on the first steps of data analysis, for example identifying variants, supported by EPI2ME software and a wide range of pre-configured workflows, including one focusing on human genomic and epigenomic variation. The partnership with Saphetor will offer another layer of tertiary analysis focused on genetic variants and the prioritisation of those likely linked to conditions.

VarSome Clinical offers high quality visualisation capabilities that include co-visualisation of different variant categories in a single view for a given region of interest, categorised with variant predicted impact, phase information (if available) and co-location from other known variants in that region from publicly available databases. It also delivers a sample viewer that provides a simple, filterable view of overall landscape of variation in the sample under analysis. Additionally, it allows for active and dynamic filtering of data in real time with ability to save and re-use named filters.

To begin with, the end-to-end solution will focus on the analysis of long-read whole genome sequencing for rare and undiagnosed diseases, initially in the clinical research setting. Once validated, the platform is expected to enhance the future clinical use of the information rich data produced by Oxford Nanopore enabling variant discovery, annotation, and classification.

Gordon Sanghera, CEO, Oxford Nanopore Technologies, commented:

“We are excited to collaborate with Saphetor to provide end-to-end solutions for our customers. Combining long nanopore sequencing reads with Saphetor’s comprehensive tertiary analysis for clinical researchers in cancer, and rare and undiagnosed diseases will be hugely impactful and will support future clinical use with information rich data.”

Andreas Massouras, CEO, Saphetor SA, commented:

The potential of long read sequencing in the clinical setting is tremendous. It could have a great impact for both cancer and rare conditions by bringing structural variants into play as part of clinical decision making. Oxford Nanopore have been pioneering in the sequencing space for a number of years now - to be part of their continued success is very exciting, and we are greatly looking forward to helping accelerate the adoption of long read sequencing technologies into the clinic so that early adopters can start to establish clinical utility and advance genomic healthcare.

If you are interested in learning more about Saphetor and the VarSome Clinical solution, it will be demonstrated during the upcoming American Society of Human Genomics (ASHG) conference, in Washington DC, in November. Further information here.

If you are interested in discussing more about our product or what we do to support clinical research, contact your nanopore representative.