Thermo Fisher Scientific Introduces First Next-Generation Sequencing Platform

on Torrent Genexus System* holds potential to advance precision medicine in the clinic

Thermo Fisher Scientific announced the launch of its Ion Torrent Genexus System, the first fully integrated, next-generation sequencing (NGS) platform featuring an automated specimen-to-report workflow that delivers results economically in a single day. Launched at the Association for Molecular Pathology (AMP) 2019 annual meeting, this turnkey solution redefines the genomic profiling paradigm and enables a future in which local hospitals can adopt NGS testing. The company also introduced its Oncomine Precision Assay*, an innovative pan-cancer panel for the Genexus platform. It enables comprehensive genomic profiling from formalin-fixed, paraffin-embedded (FFPE) tissue and liquid biopsy samples with a single assay.

“Our goal is to advance precision medicine in every clinical setting by enabling clinicians to leverage the power of comprehensive genomic information,” said Mark Stevenson, executive vice president and chief operating officer at Thermo Fisher Scientific. “We can envision a time when patients at local hospitals will have faster access to comprehensive test results that can guide more effective, targeted therapy selection and improved health outcomes.”

A recent study in the journal Clinical Lung Cancer1 underscores the logistical challenges that limit local hospitals from providing NGS-based genomic testing today even though that is where most patients are treated. Due to NGS adoption barriers, including product complexity and cost, the vast majority of local molecular laboratories rely on limited single-gene tests. Since this testing approach does not provide a complete genomic profile of a tumor, some laboratories choose to outsource sample testing for more comprehensive NGS analysis.

Outsourced NGS testing by reference laboratories that use other on-market NGS platforms are plagued by two major issues: results that take several weeks, as highlighted in a Cancers2 article, and larger sample input requirements. Stringent sample requirements often lead to quantity not sufficient (QNS) reports, meaning results are inconclusive. Cancer clinical research studies3-6 published this year show QNS rates ranging from 17 to 23 percent, excluding samples not submitted because they failed to meet sample quantity criteria. These issues are often incompatible with timely treatment decisions and can lead to poor clinical outcomes.

Unprecedented Turnaround Time and Automation
The Genexus System changes the current paradigm. Its unprecedented turnaround time and fully automated workflow minimize user intervention and the potential for human error. The system also requires minimal amounts of tissue sample and can run small batches cost-effectively to deliver a comprehensive report in one day. Together, these features set the stage for molecular pathologists in the future to analyze NGS information in parallel with first-line testing modalities, such as immunohistochemistry (IHC).

Thermo Fisher Scientific Genexus

The Genexus System features unprecedented speed and automation to deliver next-generation sequencing results in one day (Image credit:Thermo Fisher Scientific)

“The speed is amazing, but to me, the real value of the Genexus System is how easy it is to use,” said early access user Jose Luis Costa, Ph.D., principal investigator, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP). “Newcomers who have yet to adopt NGS because they believe it is too difficult will find that the Genexus System takes away all the complexity. This is the first system that will go from a biological sample to a report with practically zero intervention from the operator.”

Laboratories can scale their sequencing runs with an innovative sequencing chip design that will enable in-house sequencing facilities to cost-effectively process small batches of samples as they arrive at the lab. The Genexus System includes the Genexus Integrated Sequencer, the Genexus Purification System and an onboard reporting software.

The system and its associated reagents are manufactured in an ISO 13485 facility that is registered with the U.S. Food and Drug Administration (FDA). Thermo Fisher plans to seek FDA approval of the Genexus System to accelerate future development of a broad menu of diagnostic assays in oncology and other clinical applications.

Biomarker Testing for Solid Tissue and Liquid Biopsy Cancer Samples With a Single Assay
The Oncomine Precision Assay maximizes detection of relevant biomarkers, such as EGFR, ALK, KRAS, BRAF, ROS1, NTRK, RET, HER2, ERBB2 and others, via sequencing from FFPE and liquid biopsy samples. When combined with the Genexus System, molecular testing laboratories will soon be able to generate comprehensive NGS results within the same timeframe as single-gene tests. The assay marks the first of several panels planned for oncology studies and other research application areas, including infectious disease, inherited disease and reproductive health.

“The advances enabled by the Genexus System are exemplary of the significant progress in next-generation sequencing over the last two decades,” said Dr. Yusuke Nakamura, program director, who leads the AI Hospital Project, a national program to establish liquid biopsy screening using NGS and qPCR in Japan. “The full automation of this new system will transform cancer research and clinical management, and enable NGS testing to be more broadly accessible to decentralized labs in the future.”

For more information on the Genexus System and Oncomine Precision Assay, please visit Thermo Fisher’s booth (#2825) at AMP, or visit the company website.

1. Genomic Profiling of Advanced Non-Small Cell Lung Cancer in Community Settings: Gaps and Opportunities; Martin E. Gutierrez, et al.; Clinical Lung Cancer, Nov. 2017.

2. In-house Implementation of Tumor Mutational Burden Testing to Predict Durable Clinical Benefit in Non-small Cell Lung Cancer and Melanoma Patients. Heeke S. et al. Cancers. Aug. 2019;11(9). pii: E1271. doi: 10.3390/cancers11091271.

3. Next-Generation Sequencing in 305 Consecutive Patents: Clinical Outcomes and Management Changes; Gregory J. Kubicek, MD., et al., Journal of Clinical Oncology, Aug. 2019.

4. First-Line Nivolumab Plus Ipilimumab in Advanced Non-Small-Cell Lung Cancer (CheckMate 568): Outcomes by Programmed Death Ligand 1 and Tumor Mutational Burden as Biomarkers; Suresh S. Ramalingam, MD., et al., Journal of Oncology, Feb. 2019.

5. Clinical utility of FoundationOne tissue molecular profiling in men with metastatic prostate cancer; Jason Zhu, et al.; Urologic Cancer: Seminars and Original Investigations, July 2019.

6. Abstract 4889: Comparison of tumor mutational burden using the Ion Oncomine™ TML and FoundationOne™ assays with routine clinical FFPE tissue samples to predict durable clinical benefit in lung cancer and melanoma patients – a multivariate analysis integrating PD-L1 and CD8+ evaluation. Heeke S. et al. DOI: 10.1158/1538-7445.AM2019-4889; July 2019.

*For research use only. Not for use in diagnostic procedures

About Thermo Fisher Scientific
Thermo Fisher Scientific Inc. is the world leader in serving science, with revenues of more than $24 billion and approximately 70,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics, deliver medicines to market and increase laboratory productivity. Through our premier brands – Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific and Unity Lab Services – we offer an unmatched combination of innovative technologies, purchasing convenience and comprehensive support. For more information, please visit


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