Key Advancement in Cancer Sequencing: Development of Next-Generation Sequencing for Somatic Mutation Detection

In advance of the 2016 American Molecular Pathology (AMP) meeting, Swift Biosciences, Inc. and Fluxion Biosciences, Inc. announced a key advancement in cancer sequencing. Improving the sensitivity to detect mutations at very low frequencies using low input samples.

This advancement will help enable the use of liquid biopsies to better characterize cancer progression. Liquid biopsies represent a major breakthrough in the ability to detect molecular changes in tumor progression without the need for a tissue biopsy. Unlike a tissue biopsy that can only be characterized once, liquid biopsy samples can be routinely obtained during the course of treatment, providing insight into the cancer’s progression. These samples offer the potential to characterize cancer in real time using only a routine blood draw. Until recently, this approach has been limited by the available amount of tumor DNA that can be recovered from peripheral blood samples.

To achieve this advancement, the two companies worked together to integrate Fluxion’s IsoFlux™ System and ERASE-Seq software with Swift’s Accel-Amplicon™ technology to create a workflow for the detection of variants to levels of > 0.1% frequency from sample inputs as low as 200 cells. The IsoFlux System enriches rare tumor cells circulating in the blood by using a combination of epithelial and mesenchymal markers. DNA isolated from these cells can now be enriched for oncology targets using the Spotlight 59 gene panel, powered by Swift’s Accel-Amplicon technology, to then be sequenced using the Illumina or Ion Torrent next generation sequencing (NGS) platforms. The subsequent data is then analyzed with the ERASE-Seq (Elimination of Recurrent Artifacts and Stochastic Errors) software, enabling the detection of mutations well below the 1.0% threshold. This system can detect somatic mutations in circulating tumor cells, circulating cell-free DNA (cfDNA), and may even be applied to other challenging sample types such as FFPE. Details of the product workflow and data will be jointly presented by both firms at AMP.

Speaking about the successful product launch, Jeff Jensen, CEO of Fluxion stated, “We are excited about the overall performance of the workflow that offers clinical researchers the ability to go from whole blood to sequencer-ready libraries in under a day. Swift’s ability to create a single-tube amplicon panel for Fluxion enables researchers to use the preciously small amounts of inputs in the most economical method.”

“The combination of technologies from our two companies provides a real advancement for researchers in the cancer sequencing community,” stated Timothy Harkins, PhD., President and CEO of Swift Biosciences. “There has been a sensitivity barrier for next generation sequencing to detect low frequency mutations, and often that threshold has been in the 1% to 5% range. Fluxion has made a significant improvement with their ERASE-Seq software to break through that sensitivity barrier, getting down to the 0.1% threshold, which puts NGS on par with many other genetic tools.”