Thermo Fisher Launches Ion Torrent Genexus System: First Fully Integrated NGS Platform Delivering Specimen-to-Report in a Single Day

This week, Thermo Fisher Scientific (hereinafter referred to as “Thermo Fisher”), a supplier in the U.S. scientific services sector, released at the 2019 Annual Meeting of the Association for Molecular Pathology (AMP)Its first high-throughput next-generation sequencing (NGS) platform capable of automatically completing the entire workflow from sample preparation to result reporting within a single day—the Ion Torrent Genexus System.On the same day, Thermo Fisher Scientific also released accessories compatible with this systemOncomine Precision Assay Pan-Cancer Panel, enabling comprehensive genomic analysis of FFPE tissue samples or liquid biopsy specimens through a single assay.

“Our goal is to advance precision medicine in every clinical setting by empowering clinicians to fully leverage the power of comprehensive genomic information.”Mark Stevenson, Executive Vice President and Chief Operating Officer of Thermo Fisher Scientificstated, “We can anticipate that patients at primary care hospitals will have faster access to comprehensive test results in the future, thereby guiding more effective and targeted treatment choices and improving health outcomes.”

Reportedly, as Thermo Fisher Scientific’s first fully integrated NGS platform, the Ion Torrent Genexus System provides a one-day, one-stop automated end-to-end solution. This platform enables the complete gene sequencing workflow—from sample to report—to be performed automatically and cost-effectively within a single day using only a small number of samples, with virtually no manual intervention required. This facilitates the establishment of in-house NGS platforms at primary-care hospitals in the future, thereby promoting the widespread clinical adoption of precision medicine.

At a symposium hosted by the company during the AMP Annual Meeting,Andy Felton, Vice President of Product Management at Thermo Fisher Scientific, stated, The goal of the Ion Torrent Genexus System is to enable primary care hospitals to perform NGS testing in-house, which is essential for realizing the vision of precision medicine.

Currently, due to the complexity and cost of next-generation sequencing (NGS) testing, the vast majority of primary-care molecular laboratories still rely on limited single-gene assays. However, this approach fails to provide comprehensive tumor genomic profiling; consequently, some laboratories choose to outsource sample testing for more extensive NGS analysis. At the symposium, researchers cited a study published last year by Flatiron Health. The study indicated that many patients, despite undergoing comprehensive genomic profiling and having actionable mutations detected, did not receive targeted therapy, at least within community healthcare settings. Experts at the meeting speculated that this disparity might be attributable to prolonged turnaround times or clinicians’ skepticism toward outsourced testing. These issues often lead to adverse clinical outcomes. Thermo Fisher Scientific believes that this sequencing system will help facilitate the adoption of NGS in more hospital laboratories, thereby addressing these challenges.

However, the Ion Torrent Genexus system is not the only sequencing platform that markets itself on a “sample-to-result” end-to-end workflow. Previously, Qiagen’s GeneReader sequencer also emphasized this concept, but Qiagen has now decided to discontinue development of this instrument. Andy Felton stated,Unlike previous systems that attempted a “sample-to-result” workflow, the Ion Torrent Genexus is a more highly integrated system: housed in two instruments and fully automated, making it more attractive to smaller primary-care hospitals., while other products marketed as “sample-to-result” solutions still require three or more instruments in series.

The Ion Torrent Genexus system comprises two separate instruments: the first is an automated nucleic acid extraction, purification, and quantification system, which is not yet priced; the second instrument performs all tasks from library preparation and sequencing to clinical reporting, with a listed price of $299,000. The front-end sample instrument can process a wide variety of specimen types, including FFPE tissues, plasma, bone marrow, and blood. Furthermore, each GX5 sequencing chip in the system features four independent channels, with each channel generating 12 to 15 million reads. Andy Felton stated, “We have also introduced fully automated library preparation for AmpliSeq and AmpliSeq HD, capable of handling up to 32 libraries.” Each chip can simultaneously support up to four different assays; if the chemistry is identical, users can perform DNA and RNA assays concurrently. A single channel completes its entire workflow within 14 hours, while a full chip run takes approximately 24 to 30 hours. The overall design of the system aims to enable rapid runs, bringing the turnaround time for NGS results closer to that of single-gene tests and other laboratory procedures.

Notably, the system also employs new software for the analysis and reporting of test results. Andy Felton stated that this represents the first major update to the analysis software since the launch of the first-generation Ion Torrent PGM in 2010. “In essence, we have integrated the former Torrent Suite software and Ion Reporter into a single Genexus System Software, guiding users from run setup through variant detection and annotation, and finally into our Oncomine Knowledgebase Reporting Tool to generate clinical reports,” he explained. He added that Thermo Fisher Scientific has made significant efforts to ensure that the system can operate efficiently and cost-effectively with fewer samples, while maintaining flexibility and the capacity to handle higher sample volumes. “Compared to our current GeneStudio S5 System, we anticipate an approximately 50% reduction in per-sample cost when processing batches of four samples on this system,” Andy Felton added.

References:

1. Thermo Fisher Scientific Introduces First Next-Generation Sequencing Platform That Delivers Specimen to Report in a Single Day

2. Thermo Fisher Launches Genexus Sequencing System to Support Local Deployment of NGS

3. Thermo Fisher's automated sequencer to offer same-day, pan-cancer test results