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Next-generation Sequencing: From Specimen to Report in a Single Day

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Thermo Fisher Scientific has announced the launch of its Ion Torrent Genexus System, a fully integrated, next-generation sequencing (NGS) platform featuring an automated specimen-to-report workflow that can deliver results in a single day. Launched at the Association for Molecular Pathology (AMP) 2019 annual meeting, this system aims to redefine the genomic profiling paradigm and enable 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 Cancer 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 can experience two major issues: results that take several weeks and larger sample input requirements. Stringent sample requirements often lead to quantity not sufficient (QNS) reports, meaning results are inconclusive. These issues are often incompatible with timely treatment decisions and can lead to poor clinical outcomes.

The Genexus System aims to solve these problems. Its turnaround time and fully automated workflow are designed to 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. 

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.

Biomarker Testing for Solid Tissue and Liquid Biopsy Cancer Samples With a Single Assay

The Oncomine Precision Assay aims to maximize 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 could 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.