Application Note - Somatic variant detection from circulating tumor cell samples using NGS

OVERVIEW

  • The IsoFlux System (Fluxion Biosciences) enables non-invasive circulating tumor cell (CTC) access to provide real-time and frequent monitoring of cancer disease progression while avoiding the risks and burden of tumor biopsies.
  • Following CTC enrichment and purification using the IsoFlux System, mutational profiling of 50 oncogenes and tumor suppressor genes was achieved using the Ion AmpliSeq™ Cancer Hotspot Panel v2. Sequencing on the Ion PGM™ System and simple bioinformatics with Ion Reporter™ Software help streamline the analysis of critical cancer variants.
  • Variant detection with NGS is possible from as few as 2 CTCs per 1 mL of blood. This level of CTC recovery is routinely achieved with the IsoFlux System (>70% of samples tested to date from multiple solid tumor types, including breast, lung, colorectal, prostate, and pancreatic cancers).
  • Using analytical validation samples, CTC enrichment using the IsoFlux NGS DNA Kit resulted in tumor cell purity ranging from 5-22%. Blinded, standardized analysis using a custom variant filter resulted in detection of all cell line variants (single nucleotide variants, SNVs) down to a concentration of 2 cells/mL, and a mutant allelic frequency of 2%, with 95% specificity.
  • The results presented here indicate that the IsoFlux System, Ion AmpliSeq™ technology, and the Ion PGM™ System offer a superior workflow for translational oncology studies.

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